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-<h1 id="arhgef1">ARHGEF1</h1>
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-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">Tier</th>
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-<th>Description</th>
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-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
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-<td style="text-align:center">2</td>
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-<td>relevance in BL not firmly established</td>
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-</tr>
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-</tbody>
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-</table>
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-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">source</th>
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-<th style="text-align:center">frequency (%)</th>
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-</tr>
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-</thead>
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-<tbody>
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-<tr>
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-<td style="text-align:center">BL</td>
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-<td style="text-align:center">GAMBL genomes+capture</td>
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-<td style="text-align:center">3.93</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">BL</td>
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-<td style="text-align:center">Thomas cohort</td>
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-<td style="text-align:center">2.00</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">BL</td>
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-<td style="text-align:center">Panea cohort</td>
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-<td style="text-align:center">NA</td>
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-</tr>
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-</tbody>
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-</table>
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-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">aSHM</th>
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-<th style="text-align:center">Significant selection</th>
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-<th style="text-align:center">dN/dS (missense)</th>
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-<th style="text-align:center">dN/dS (nonsense)</th>
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-<td style="text-align:center">BL</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">2.954</td>
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-<td style="text-align:center">0.000</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">2.662</td>
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-<td style="text-align:center">9.372</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">FL</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">3.865</td>
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-<td style="text-align:center">0.000</td>
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-</tr>
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-</tbody>
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-</table>
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-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1_protein_hg38.html">hg38</a></p>
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-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARHGEF1_NM_199002.svg" alt="image"></p>
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-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1_hg38.html">hg38</a></p>
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-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARHGEF1.svg" alt="image"></p>
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-<h2 id="arhgef1-expression">ARHGEF1 Expression</h2>
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-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/ARHGEF1_by_pathology.svg" alt="image"></p>
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-<!-- ORIGIN: muppidiLossSignalingGa132014b -->
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-<!-- BL: muppidiLossSignalingGa132014b -->
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-<h2 id="references">References</h2>
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-<ol>
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-<li>Muppidi J, Schmitz R, Green JA, Green JA, Xiao W, Larsen AB, Braun S, An J, Xu Y, Rosenwald A, Ott G, Gascoyne R, Rimsza L, Campo E, Jaffe E, Delabie J, Smeland E, Braziel R, Tubbs R, Cook J, Weisenburger D, Chan W, Vaidehi N, Staudt L, Cyster J. Loss of signaling via Gα13 in germinal center B cell-derived lymphoma. Nature. 2014;516:254–258.</li>
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-</ol>
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BL_genes_with_bib.md
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-# BL genes
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-
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-## Origins of BL genes![sankey](BL_sankey-1.svg)
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-
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-## Tier 1 BL genes
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-
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-| Gene | Tier | Relevant references |
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-|:------------------:|:----:|:-------------------------------------------------------------:|
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-| [ARID1A](ARID1A) | 1 | (Love et al. 2012; Krysiak et al. 2017; Zhang et al. 2013) |
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-| [BMP7](BMP7) | 1 | (Panea et al. 2019) |
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-| [CCND3](CCND3) | 1 | (Morin et al. 2011; Richter et al. 2012) |
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-| [CHD8](CHD8) | 1 | (Grande et al. 2019; Reddy et al. 2017) |
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-| [DDX3X](DDX3X) | 1 | (Schmitz et al. 2012, 2018) |
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-| [EIF4A1](EIF4A1) | 1 | (Panea et al. 2019) |
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-| [EPPK1](EPPK1) | 1 | (Panea et al. 2019) |
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-| [FBXO11](FBXO11) | 1 | (Hübschmann et al. 2021; Richter et al. 2012) |
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-| [FOXO1](FOXO1) | 1 | (Schmitz et al. 2012; Morin et al. 2011) |
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-| [GNA13](GNA13) | 1 | (Love et al. 2012; Morin et al. 2011) |
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-| [GNAI2](GNAI2) | 1 | (Grande et al. 2019; Morin et al. 2013) |
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-| [HNRNPU](HNRNPU) | 1a | (Reddy et al. 2017; Panea et al. 2019) |
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-| [ID3](ID3) | 1 | (Schmitz et al. 2012; Richter et al. 2012) |
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-| [KMT2D](KMT2D) | 1 | (Morin et al. 2011; Grande et al. 2019) |
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-| [MYC](MYC) | 1a | (Johnston and Carroll 1992; L. Pasqualucci et al. 2001) |
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-| [P2RY8](P2RY8) | 1 | (Muppidi et al. 2014; Lohr et al. 2012) |
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-| [PHF6](PHF6) | 1 | (Reddy et al. 2017; Thomas et al. 2023) |
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-| [PTEN](PTEN) | 1 | (Love et al. 2012) |
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-| [RFX7](RFX7) | 1 | (Grande et al. 2019) |
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-| [RHOA](RHOA) | 1 | (Richter et al. 2012) |
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-| [SIN3A](SIN3A) | 1 | (Grande et al. 2019) |
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-| [SMARCA4](SMARCA4) | 1 | (Krysiak et al. 2017; Richter et al. 2012; Zhang et al. 2013) |
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-| [TCF3](TCF3) | 1 | (Schmitz et al. 2012) |
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-| [TCL1A](TCL1A) | 1 | (Grande et al. 2019) |
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-| [TFAP4](TFAP4) | 1 | (Grande et al. 2019) |
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-| [TP53](TP53) | 1 | (Morin et al. 2011; Wilda et al. 2004) |
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-| [USP7](USP7) | 1 | (Grande et al. 2019) |
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-| [WNK1](WNK1) | 1 | (Hübschmann et al. 2021; Thomas et al. 2023) |
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-
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-## Tier 2 BL genes
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-
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-| Gene | Tier | Relevant references |
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-|:----------------------:|:----:|:-------------------------------------------------------------------:|
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-| [ACAD9](ACAD9) | 2 | (Love et al. 2012) |
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-| [ACE](ACE) | 2 | (Love et al. 2012) |
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-| [ADAMTS5](ADAMTS5) | 2 | (Burkhardt et al. 2022) |
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-| [ADNP](ADNP) | 2 | (Burkhardt et al. 2022) |
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-| [AGO4](AGO4) | 2 | (Burkhardt et al. 2022) |
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-| [ALPK2](ALPK2) | 2 | (Panea et al. 2019) |
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-| [ARHGEF1](ARHGEF1) | 2 | (Muppidi et al. 2014) |
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-| [ATP2C2](ATP2C2) | 2 | (Love et al. 2012) |
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-| [BACH2](BACH2) | 2a | (Grande et al. 2019) |
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-| [BCL2](BCL2) | 2a | (Burkhardt et al. 2022; Morin et al. 2011; Tanaka et al. 1992) |
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-| [BCL6](BCL6) | 2a | (Love et al. 2012; Morin et al. 2011) |
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-| [BCL7A](BCL7A) | 2a | (Grande et al. 2019; Krysiak et al. 2017; Arthur et al. 2018) |
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-| [BRAF](BRAF) | 2 | (Love et al. 2012; Tiacci et al. 2011) |
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-| [BRD4](BRD4) | 2 | (Love et al. 2012) |
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-| [BTG1](BTG1) | 2a | (Morin et al. 2011; Burkhardt et al. 2022) |
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-| [BTG2](BTG2) | 2a | (Love et al. 2012; Morin et al. 2011) |
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-| [C16orf48](C16orf48) | 2 | (Schmitz et al. 2012) |
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-| [C6orf27](C6orf27) | 2 | (Love et al. 2012) |
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-| [CAD](CAD) | 2 | (Love et al. 2012) |
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-| [CARD11](CARD11) | 2 | (Lenz et al. 2008; Morin et al. 2011; Panea et al. 2019) |
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-| [CARD4](CARD4) | 2 | (Love et al. 2012) |
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-| [CCNF](CCNF) | 2 | (Abate et al. 2015) |
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-| [CCT6B](CCT6B) | 2 | (Love et al. 2012) |
65
-| [CD79A](CD79A) | 2 | (Burkhardt et al. 2022) |
66
-| [CD79B](CD79B) | 2 | (Morin et al. 2011; Panea et al. 2019) |
67
-| [CD83](CD83) | 2a | (Morin et al. 2013; Panea et al. 2019; Russler-Germain et al. 2023) |
68
-| [CDC73](CDC73) | 2 | (Reddy et al. 2017; Love et al. 2012) |
69
-| [CDH17](CDH17) | 2 | (Love et al. 2012) |
70
-| [CDKN2A](CDKN2A) | 2 | (Morin et al. 2013; Grande et al. 2019) |
71
-| [CDKN2C](CDKN2C) | 2 | (Thomas et al. 2023) |
72
-| [CHD4](CHD4) | 2 | (Burkhardt et al. 2022) |
73
-| [COL4A2](COL4A2) | 2 | (Love et al. 2012) |
74
-| [CPXM2](CPXM2) | 2 | (Burkhardt et al. 2022) |
75
-| [CREBBP](CREBBP) | 2 | (Love et al. 2012; Laura Pasqualucci, Dominguez-Sola, et al. 2011) |
76
-| [CTCF](CTCF) | 2 | (Panea et al. 2019) |
77
-| [CXCR4](CXCR4) | 2a | (Krysiak et al. 2017; Khodabakhshi et al. 2012; Panea et al. 2019) |
78
-| [CYB5D1](CYB5D1) | 2 | (Love et al. 2012) |
79
-| [CYP4F22](CYP4F22) | 2 | (Love et al. 2012) |
80
-| [DHCR7](DHCR7) | 2 | (Schmitz et al. 2012) |
81
-| [DLGAP1](DLGAP1) | 2 | (Love et al. 2012) |
82
-| [DNMT1](DNMT1) | 2 | (Panea et al. 2019) |
83
-| [DTX1](DTX1) | 2a | (Panea et al. 2019; Schmitz et al. 2018) |
84
-| [E2F2](E2F2) | 2 | (Burkhardt et al. 2022) |
85
-| [EBF1](EBF1) | 2a | (Bohle et al. 2013; Thomas et al. 2023) |
86
-| [EDNRB](EDNRB) | 2 | (Burkhardt et al. 2022) |
87
-| [EHD1](EHD1) | 2 | (Thomas et al. 2023) |
88
-| [EIF2C4](EIF2C4) | 2 | (Love et al. 2012) |
89
-| [ELP2](ELP2) | 2 | (Schmitz et al. 2012) |
90
-| [EML2](EML2) | 2 | (Love et al. 2012) |
91
-| [ENTPD3](ENTPD3) | 2 | (Love et al. 2012) |
92
-| [EP300](EP300) | 2 | (Laura Pasqualucci, Dominguez-Sola, et al. 2011; Panea et al. 2019) |
93
-| [EPHB2](EPHB2) | 2 | (Love et al. 2012) |
94
-| [ERAP1](ERAP1) | 2 | (Burkhardt et al. 2022) |
95
-| [ETS1](ETS1) | 2a | (Panea et al. 2019; Morin et al. 2011) |
96
-| [EXOSC6](EXOSC6) | 2 | (Schmitz et al. 2012) |
97
-| [EZH2](EZH2) | 2 | (Morin et al. 2010; Love et al. 2012) |
98
-| [FAM129B](FAM129B) | 2 | (Love et al. 2012) |
99
-| [FGFR3](FGFR3) | 2 | (Love et al. 2012) |
100
-| [FLYWCH1](FLYWCH1) | 2 | (Schmitz et al. 2012) |
101
-| [FTCD](FTCD) | 2 | (Love et al. 2012) |
102
-| [FZD3](FZD3) | 2 | (Panea et al. 2019) |
103
-| [GGTLA4](GGTLA4) | 2 | (Love et al. 2012) |
104
-| [GRB2](GRB2) | 2 | (Laura Pasqualucci, Trifonov, et al. 2011; Panea et al. 2019) |
105
-| [GRIK5](GRIK5) | 2 | (Love et al. 2012) |
106
-| [GTSE1](GTSE1) | 2 | (Schmitz et al. 2012) |
107
-| [HIST1H1C](HIST1H1C) | 2a | (Panea et al. 2019; Morin et al. 2011) |
108
-| [HIST1H1E](HIST1H1E) | 2a | (Morin et al. 2013; Grande et al. 2019; Krysiak et al. 2017) |
109
-| [HIST1H2AG](HIST1H2AG) | 2a | (Morin et al. 2013; Krysiak et al. 2017; Panea et al. 2019) |
110
-| [HIST1H2AM](HIST1H2AM) | 2a | (Panea et al. 2019; Krysiak et al. 2017) |
111
-| [HIST1H2BK](HIST1H2BK) | 2a | (Panea et al. 2019) |
112
-| [HIST1H3D](HIST1H3D) | 2a | (Panea et al. 2019) |
113
-| [HIST1H3H](HIST1H3H) | 2a | (Panea et al. 2019) |
114
-| [HIST1H3I](HIST1H3I) | 2a | (Panea et al. 2019; Krysiak et al. 2017) |
115
-| [HIST1H3J](HIST1H3J) | 2a | (Panea et al. 2019) |
116
-| [HIST1H4J](HIST1H4J) | 2a | (Panea et al. 2019) |
117
-| [HLA-A](HLA-A) | 2 | |
118
-| [HLA-B](HLA-B) | 2 | |
119
-| [HLA-DMB](HLA-DMB) | 2 | |
120
-| [HLA-DQB1](HLA-DQB1) | 2 | (Burkhardt et al. 2022) |
121
-| [ICK](ICK) | 2 | (Love et al. 2012) |
122
-| [IGLL5](IGLL5) | 2a | (Russler-Germain et al. 2023; Panea et al. 2019) |
123
-| [IKZF3](IKZF3) | 2a | (Panea et al. 2019; Morin et al. 2013) |
124
-| [IRF8](IRF8) | 2a | (Panea et al. 2019; Morin et al. 2011) |
125
-| [ITPR3](ITPR3) | 2 | (Love et al. 2012) |
126
-| [KANK2](KANK2) | 2 | (Schmitz et al. 2012) |
127
-| [KCNK10](KCNK10) | 2 | (Panea et al. 2019) |
128
-| [KIFC3](KIFC3) | 2 | (Love et al. 2012) |
129
-| [KLHL26](KLHL26) | 2 | (Burkhardt et al. 2022) |
130
-| [KLHL6](KLHL6) | 2a | (Morin et al. 2011; Panea et al. 2019) |
131
-| [KMT2C](KMT2C) | 2 | (Zhou et al. 2019; Zhang et al. 2013) |
132
-| [LTB](LTB) | 2a | (Panea et al. 2019; Chapuy et al. 2018) |
133
-| [MAP3K6](MAP3K6) | 2 | (Love et al. 2012) |
134
-| [MCL1](MCL1) | 2 | (Panea et al. 2019; Reddy et al. 2017) |
135
-| [MIR142](MIR142) | 2a | (Grande et al. 2019; Kwanhian et al. 2012) |
136
-| [MKI67](MKI67) | 2 | (Russler-Germain et al. 2023; Schmitz et al. 2012) |
137
-| [MME](MME) | 2 | (Panea et al. 2019) |
138
-| [MTOR](MTOR) | 2 | (Zhang et al. 2013; Panea et al. 2019) |
139
-| [MYH10](MYH10) | 2 | (Love et al. 2012) |
140
-| [MYO18A](MYO18A) | 2 | (Schmitz et al. 2012) |
141
-| [NBEAL1](NBEAL1) | 2 | (Love et al. 2012) |
142
-| [NCOR2](NCOR2) | 2 | (Schmitz et al. 2012) |
143
-| [NOA1](NOA1) | 2 | (Burkhardt et al. 2022) |
144
-| [NOTCH1](NOTCH1) | 2 | (Laura Pasqualucci, Trifonov, et al. 2011; Love et al. 2012) |
145
-| [NOTCH2](NOTCH2) | 2 | (Trøen et al. 2008; Panea et al. 2019) |
146
-| [NRXN2](NRXN2) | 2 | (Love et al. 2012) |
147
-| [P2RY2](P2RY2) | 2 | (Love et al. 2012) |
148
-| [PABPC4L](PABPC4L) | 2 | (Panea et al. 2019) |
149
-| [PC](PC) | 2 | (Love et al. 2012) |
150
-| [PCBP1](PCBP1) | 2 | (Schmitz et al. 2012) |
151
-| [PCDHA11](PCDHA11) | 2 | (Panea et al. 2019) |
152
-| [PDCD11](PDCD11) | 2 | (Schmitz et al. 2012) |
153
-| [PDZRN3](PDZRN3) | 2 | (Panea et al. 2019) |
154
-| [PIK3R1](PIK3R1) | 2 | (Zhang et al. 2013; Panea et al. 2019) |
155
-| [PIM1](PIM1) | 2a | (L. Pasqualucci et al. 2001; Burkhardt et al. 2022) |
156
-| [PLCG2](PLCG2) | 2 | (Panea et al. 2019) |
157
-| [POLRMT](POLRMT) | 2 | (Love et al. 2012) |
158
-| [POR](POR) | 2 | (Love et al. 2012) |
159
-| [PPP6R2](PPP6R2) | 2 | (Burkhardt et al. 2022) |
160
-| [PREX1](PREX1) | 2 | (Burkhardt et al. 2022) |
161
-| [PRSS22](PRSS22) | 2 | (Love et al. 2012) |
162
-| [PTPRN](PTPRN) | 2 | (Love et al. 2012) |
163
-| [PXDNL](PXDNL) | 2 | (Panea et al. 2019) |
164
-| [RAC2](RAC2) | 2 | (Hübschmann et al. 2021; Panea et al. 2019) |
165
-| [RANBP6](RANBP6) | 2 | (Love et al. 2012) |
166
-| [RBP3](RBP3) | 2 | (Love et al. 2012) |
167
-| [RET](RET) | 2 | (Love et al. 2012) |
168
-| [REV3L](REV3L) | 2 | (Burkhardt et al. 2022) |
169
-| [RNF144B](RNF144B) | 2 | (Panea et al. 2019) |
170
-| [RPL10](RPL10) | 2 | (Burkhardt et al. 2022) |
171
-| [S1PR2](S1PR2) | 2a | (Morin et al. 2011; Muppidi et al. 2014) |
172
-| [SAL3](SAL3) | 2 | (Burkhardt et al. 2022) |
173
-| [SALL3](SALL3) | 2 | (Love et al. 2012) |
174
-| [SAPS2](SAPS2) | 2 | (Love et al. 2012) |
175
-| [SBF1](SBF1) | 2 | (Love et al. 2012) |
176
-| [SF3B1](SF3B1) | 2 | (Love et al. 2012) |
177
-| [SHANK1](SHANK1) | 2 | (Love et al. 2012) |
178
-| [SLC29A2](SLC29A2) | 2 | (Love et al. 2012) |
179
-| [SNTB2](SNTB2) | 2 | (Panea et al. 2019) |
180
-| [SP3](SP3) | 2 | (Panea et al. 2019) |
181
-| [SYNCRIP](SYNCRIP) | 2 | (Panea et al. 2019) |
182
-| [SYNGAP1](SYNGAP1) | 2 | (Love et al. 2012) |
183
-| [TBC1D9B](TBC1D9B) | 2 | (Love et al. 2012) |
184
-| [TET2](TET2) | 2 | (Albuquerque et al. 2017; Panea et al. 2019) |
185
-| [TIGD6](TIGD6) | 2 | (Love et al. 2012) |
186
-| [TOP2A](TOP2A) | 2 | (Schmitz et al. 2012) |
187
-| [TPST2](TPST2) | 2 | (Love et al. 2012) |
188
-| [TTN](TTN) | 2 | (Burkhardt et al. 2022) |
189
-| [VWA7](VWA7) | 2 | (Burkhardt et al. 2022) |
190
-| [WDR7](WDR7) | 2 | (Panea et al. 2019) |
191
-| [WDR90](WDR90) | 2 | (Schmitz et al. 2012) |
192
-| [WHAMM](WHAMM) | 2 | (Schmitz et al. 2012) |
193
-| [WNK2](WNK2) | 2 | (Panea et al. 2019) |
194
-| [YY1AP1](YY1AP1) | 2 | (Schmitz et al. 2012) |
195
-| [ZAN](ZAN) | 2 | (Burkhardt et al. 2022) |
196
-| [ZBTB7A](ZBTB7A) | 2 | (Burkhardt et al. 2022; Reddy et al. 2017) |
197
-| [ZFP36L1](ZFP36L1) | 2a | (Morin et al. 2011; Panea et al. 2019) |
198
-| [ZNF229](ZNF229) | 2 | (Love et al. 2012) |
199
-| [ZNF85](ZNF85) | 2 | (Burkhardt et al. 2022) |
200
-
201
-# References
202
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-<h1 id="ccdc42bpb">CCDC42BPB</h1>
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-<h2 id="history">History</h2>
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-<p>Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup></p>
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-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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-timeline
373
- title Publication timing
374
- 2021-05-05 : Hübschmann : FL
375
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-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
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-<table>
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-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/FL_tier2.png" alt="FL"></td>
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-<td style="text-align:center">2</td>
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-<td>relevance in FL not firmly established</td>
390
-</tr>
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-</tbody>
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-</table>
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-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">source</th>
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-<th style="text-align:center">frequency (%)</th>
400
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-<td style="text-align:center">FL</td>
405
-<td style="text-align:center">GAMBL genomes</td>
406
-<td style="text-align:center">NA</td>
407
-</tr>
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-</tbody>
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-</table>
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-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
411
-<p>|</p>
412
-<blockquote>
413
-<p>[!NOTE]
414
-First described in FL in 2021 by <a href="https://pubmed.ncbi.nlm.nih.gov/33953289">Hübschmann D</a></p>
415
-</blockquote>
416
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB_protein_hg38.html">hg38</a></p>
417
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB_hg38.html">hg38</a></p>
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-<h2 id="references">References</h2>
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-<ol>
423
-<li>Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491</li>
424
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-<h1 id="ccl4">CCL4</h1>
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370
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371
-<table>
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-<thead>
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-<th style="text-align:center">Entity</th>
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377
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-<tbody>
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-<tr>
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-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
382
-<td style="text-align:center">2</td>
383
-<td>relevance in DLBCL not firmly established</td>
384
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385
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386
-</table>
387
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
388
-<table>
389
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390
-<tr>
391
-<th style="text-align:center">Entity</th>
392
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-<td style="text-align:center">DLBCL</td>
399
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400
-<td style="text-align:center">0.19</td>
401
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402
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403
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404
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405
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406
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407
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409
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410
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411
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-<td style="text-align:center">DLBCL</td>
414
-<td style="text-align:center">Chapuy cohort</td>
415
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416
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417
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418
-</table>
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-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
420
-<table>
421
-<thead>
422
-<tr>
423
-<th style="text-align:center">Entity</th>
424
-<th style="text-align:center">aSHM</th>
425
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426
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428
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-<tbody>
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-<td style="text-align:center">BL</td>
433
-<td style="text-align:center">No</td>
434
-<td style="text-align:center">No</td>
435
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436
-<td style="text-align:center">0</td>
437
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438
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439
-<td style="text-align:center">DLBCL</td>
440
-<td style="text-align:center">No</td>
441
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442
-<td style="text-align:center">3.891</td>
443
-<td style="text-align:center">0</td>
444
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445
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446
-<td style="text-align:center">FL</td>
447
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448
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449
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450
-<td style="text-align:center">0</td>
451
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-<blockquote>
455
-<p>[!NOTE]
456
-First described in DLBCL in 2018 by <a href="https://pubmed.ncbi.nlm.nih.gov/29713087">Chapuy B</a></p>
457
-</blockquote>
458
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4_protein_hg38.html">hg38</a></p>
459
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CCL4_NM_002984.svg" alt="image"></p>
460
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4_hg38.html">hg38</a></p>
461
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CCL4.svg" alt="image"></p>
462
-<h2 id="ccl4-expression">CCL4 Expression</h2>
463
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/CCL4_by_pathology.svg" alt="image"></p>
464
-<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
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466
-<h2 id="references">References</h2>
467
-<ol>
468
-<li>Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387</li>
469
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-<h1 id="cd274">CD274</h1>
369
-<h2 id="overview">Overview</h2>
370
-<p>the CD274 gene encodes the programmed death-ligand 1 (PD-L1). Mutations in B-cell lymphomas, such as DLBCL, are relatively rare.<sup>1</sup> Although rare, mutations have the potential to impact PD-L1 expression and could be relevant in the context of immune checkpoint inhibitors.</p>
371
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">Tier</th>
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-<th>Description</th>
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-</tr>
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-</thead>
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-<tbody>
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-<tr>
382
-<td style="text-align:center">DLBCL</td>
383
-<td style="text-align:center">1</td>
384
-<td>high-confidence DLBCL gene</td>
385
-</tr>
386
-</tbody>
387
-</table>
388
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
389
-<table>
390
-<thead>
391
-<tr>
392
-<th style="text-align:center">Entity</th>
393
-<th style="text-align:center">source</th>
394
-<th style="text-align:center">frequency (%)</th>
395
-</tr>
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-</thead>
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-<tbody>
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-<tr>
399
-<td style="text-align:center">DLBCL</td>
400
-<td style="text-align:center">GAMBL genomes</td>
401
-<td style="text-align:center">0.96</td>
402
-</tr>
403
-<tr>
404
-<td style="text-align:center">DLBCL</td>
405
-<td style="text-align:center">Schmitz cohort</td>
406
-<td style="text-align:center">2.34</td>
407
-</tr>
408
-<tr>
409
-<td style="text-align:center">DLBCL</td>
410
-<td style="text-align:center">Reddy cohort</td>
411
-<td style="text-align:center">1.30</td>
412
-</tr>
413
-<tr>
414
-<td style="text-align:center">DLBCL</td>
415
-<td style="text-align:center">Chapuy cohort</td>
416
-<td style="text-align:center">2.56</td>
417
-</tr>
418
-</tbody>
419
-</table>
420
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
421
-<table>
422
-<thead>
423
-<tr>
424
-<th style="text-align:center">Entity</th>
425
-<th style="text-align:center">aSHM</th>
426
-<th style="text-align:center">Significant selection</th>
427
-<th style="text-align:center">dN/dS (missense)</th>
428
-<th style="text-align:center">dN/dS (nonsense)</th>
429
-</tr>
430
-</thead>
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-<tbody>
432
-<tr>
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-<td style="text-align:center">BL</td>
434
-<td style="text-align:center">No</td>
435
-<td style="text-align:center">No</td>
436
-<td style="text-align:center">5.538</td>
437
-<td style="text-align:center">0.000</td>
438
-</tr>
439
-<tr>
440
-<td style="text-align:center">DLBCL</td>
441
-<td style="text-align:center">No</td>
442
-<td style="text-align:center">No</td>
443
-<td style="text-align:center">2.633</td>
444
-<td style="text-align:center">49.045</td>
445
-</tr>
446
-<tr>
447
-<td style="text-align:center">FL</td>
448
-<td style="text-align:center">No</td>
449
-<td style="text-align:center">No</td>
450
-<td style="text-align:center">4.631</td>
451
-<td style="text-align:center">42.709</td>
452
-</tr>
453
-</tbody>
454
-</table>
455
-<blockquote>
456
-<p>[!NOTE]
457
-First described in DLBCL in 2011 by <a href="https://pubmed.ncbi.nlm.nih.gov/21796119">Morin RD</a></p>
458
-</blockquote>
459
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274_protein_hg38.html">hg38</a></p>
460
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CD274_NM_014143.svg" alt="image"></p>
461
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274_hg38.html">hg38</a></p>
462
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CD274.svg" alt="image"></p>
463
-<h2 id="references">References</h2>
464
-<ol>
465
-<li><em>Huang RSP, Decker B, Murugesan K, Hiemenz M, Mata DA, Li G, Creeden J, Ramkissoon SH, Ross JS. Pan-cancer analysis of CD274 (PD-L1) mutations in 314,631 patient samples and subset correlation with PD-L1 protein expression. J Immunother Cancer. 2021 Jun;9(6):e002558. doi: 10.1136/jitc-2021-002558. PMID: 34130989; PMCID: PMC8207995.</em></li>
466
-<li><em>Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.</em></li>
467
-</ol>
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DLBCL_genes_with_bib.md
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1
-# DLBCL genes
2
-
3
-## Origins of DLBCL genes![sankey](DLBCL_sankey-1.svg)
4
-
5
-## Tier 1 DLBCL genes
6
-
7
-| Gene | Tier | Relevant references |
8
-|:----------------------:|:----:|:-------------------------------------------------------------------:|
9
-| [ACTB](ACTB) | 1a | (Lohr et al. 2012) |
10
-| [ACTG1](ACTG1) | 1a | (Hübschmann et al. 2021) |
11
-| [ARID1A](ARID1A) | 1 | (Krysiak et al. 2017; Love et al. 2012; Zhang et al. 2013) |
12
-| [ATM](ATM) | 1 | (Reddy et al. 2017) |
13
-| [B2M](B2M) | 1 | (Morin et al. 2011) |
14
-| [BCL10](BCL10) | 1 | (Morin et al. 2011; Russler-Germain et al. 2023) |
15
-| [BCL11A](BCL11A) | 1a | |
16
-| [BCL2](BCL2) | 1a | (Tanaka et al. 1992; Morin et al. 2011; Burkhardt et al. 2022) |
17
-| [BCL6](BCL6) | 1a | (Love et al. 2012; Morin et al. 2011) |
18
-| [BCL7A](BCL7A) | 1a | (Grande et al. 2019; Krysiak et al. 2017; Arthur et al. 2018) |
19
-| [BCOR](BCOR) | 1 | |
20
-| [BCR](BCR) | 1 | |
21
-| [BIRC6](BIRC6) | 1 | (Reddy et al. 2017) |
22
-| [BRAF](BRAF) | 1 | (Love et al. 2012; Tiacci et al. 2011) |
23
-| [BTG1](BTG1) | 1a | (Burkhardt et al. 2022; Morin et al. 2011) |
24
-| [BTG2](BTG2) | 1a | (Love et al. 2012; Morin et al. 2011) |
25
-| [BTK](BTK) | 1 | (Albuquerque et al. 2017; Krysiak et al. 2017) |
26
-| [CARD11](CARD11) | 1 | (Panea et al. 2019; Morin et al. 2011; Lenz et al. 2008) |
27
-| [CASP8](CASP8) | 1 | (Reddy et al. 2017) |
28
-| [CCND3](CCND3) | 1 | (Morin et al. 2011; Richter et al. 2012) |
29
-| [CD274](CD274) | 1 | (Morin et al. 2011) |
30
-| [CD36](CD36) | 1 | (Laura Pasqualucci, Trifonov, et al. 2011) |
31
-| [CD58](CD58) | 1 | (Morin et al. 2011) |
32
-| [CD70](CD70) | 1 | (Morin et al. 2011; Russler-Germain et al. 2023) |
33
-| [CD79B](CD79B) | 1 | (Panea et al. 2019; Morin et al. 2011) |
34
-| [CD83](CD83) | 1a | (Russler-Germain et al. 2023; Panea et al. 2019; Morin et al. 2013) |
35
-| [CDKN2A](CDKN2A) | 1 | (Grande et al. 2019; Morin et al. 2013) |
36
-| [CIITA](CIITA) | 1a | (Morin et al. 2011) |
37
-| [CREBBP](CREBBP) | 1 | (Love et al. 2012; Laura Pasqualucci, Dominguez-Sola, et al. 2011) |
38
-| [CXCR4](CXCR4) | 1a | (Khodabakhshi et al. 2012; Panea et al. 2019; Krysiak et al. 2017) |
39
-| [CXCR5](CXCR5) | 1 | (Schmitz et al. 2018) |
40
-| [DAZAP1](DAZAP1) | 1 | (Pararajalingam et al. 2020) |
41
-| [DDX3X](DDX3X) | 1 | (Schmitz et al. 2018, 2012) |
42
-| [DTX1](DTX1) | 1a | (Schmitz et al. 2018; Panea et al. 2019) |
43
-| [DUSP2](DUSP2) | 1a | (Morin et al. 2013) |
44
-| [EBF1](EBF1) | 1a | (Bohle et al. 2013; Thomas et al. 2023) |
45
-| [EEF1A1](EEF1A1) | 1 | (Hübschmann et al. 2021) |
46
-| [EP300](EP300) | 1 | (Laura Pasqualucci, Dominguez-Sola, et al. 2011; Panea et al. 2019) |
47
-| [ETS1](ETS1) | 1a | (Morin et al. 2011; Panea et al. 2019) |
48
-| [ETV6](ETV6) | 1a | (Arthur et al. 2018) |
49
-| [EZH2](EZH2) | 1 | (Love et al. 2012; Morin et al. 2010) |
50
-| [FAS](FAS) | 1 | (Scholl et al. 2007) |
51
-| [FBXO11](FBXO11) | 1 | (Hübschmann et al. 2021; Richter et al. 2012) |
52
-| [FBXW7](FBXW7) | 1 | (Zhang et al. 2013) |
53
-| [FOXC1](FOXC1) | 1 | (Schmitz et al. 2018) |
54
-| [FOXO1](FOXO1) | 1 | (Schmitz et al. 2012; Morin et al. 2011) |
55
-| [GNA13](GNA13) | 1 | (Morin et al. 2011; Love et al. 2012) |
56
-| [GNAI2](GNAI2) | 1 | (Morin et al. 2013; Grande et al. 2019) |
57
-| [GRB2](GRB2) | 1 | (Panea et al. 2019; Laura Pasqualucci, Trifonov, et al. 2011) |
58
-| [GRHPR](GRHPR) | 1a | (Arthur et al. 2018) |
59
-| [HIST1H1B](HIST1H1B) | 1a | (Chapuy et al. 2018; Krysiak et al. 2017) |
60
-| [HIST1H1C](HIST1H1C) | 1a | (Panea et al. 2019; Morin et al. 2011) |
61
-| [HIST1H1D](HIST1H1D) | 1a | (Krysiak et al. 2017; Morin et al. 2013) |
62
-| [HIST1H1E](HIST1H1E) | 1a | (Grande et al. 2019; Morin et al. 2013; Krysiak et al. 2017) |
63
-| [HIST1H2AC](HIST1H2AC) | 1a | (Morin et al. 2013; Krysiak et al. 2017) |
64
-| [HIST1H2AM](HIST1H2AM) | 1a | (Panea et al. 2019; Krysiak et al. 2017) |
65
-| [HIST1H2BC](HIST1H2BC) | 1a | (Krysiak et al. 2017; Reddy et al. 2017) |
66
-| [HIST1H2BK](HIST1H2BK) | 1a | (Panea et al. 2019) |
67
-| [HIST1H3B](HIST1H3B) | 1a | (Zhang et al. 2013) |
68
-| [HIST2H2BE](HIST2H2BE) | 1a | (Schmitz et al. 2018) |
69
-| [HLA-A](HLA-A) | 1 | |
70
-| [HLA-B](HLA-B) | 1 | |
71
-| [HLA-C](HLA-C) | 1 | |
72
-| [HLA-DMA](HLA-DMA) | 1 | |
73
-| [HLA-DMB](HLA-DMB) | 1 | |
74
-| [HLA-DQA1](HLA-DQA1) | 1 | (Hübschmann et al. 2021) |
75
-| [HNRNPD](HNRNPD) | 1 | |
76
-| [HNRNPH1](HNRNPH1) | 1 | (Pararajalingam et al. 2020) |
77
-| [HNRNPU](HNRNPU) | 1 | (Panea et al. 2019; Reddy et al. 2017) |
78
-| [HVCN1](HVCN1) | 1 | (Krysiak et al. 2017) |
79
-| [IKZF3](IKZF3) | 1 | (Panea et al. 2019; Morin et al. 2013) |
80
-| [IL16](IL16) | 1 | |
81
-| [IL4R](IL4R) | 1a | (Duns et al. 2021) |
82
-| [IRF4](IRF4) | 1a | (Morin et al. 2011) |
83
-| [IRF8](IRF8) | 1a | (Panea et al. 2019; Morin et al. 2011) |
84
-| [ITPKB](ITPKB) | 1a | (Schmitz et al. 2018) |
85
-| [JUNB](JUNB) | 1 | (Reddy et al. 2017) |
86
-| [KLF2](KLF2) | 1a | (Laura Pasqualucci, Trifonov, et al. 2011) |
87
-| [KLHL14](KLHL14) | 1 | (Zhang et al. 2013) |
88
-| [KLHL6](KLHL6) | 1a | (Panea et al. 2019; Morin et al. 2011) |
89
-| [KMT2C](KMT2C) | 1 | (Zhou et al. 2019; Zhang et al. 2013) |
90
-| [KMT2D](KMT2D) | 1 | (Grande et al. 2019; Morin et al. 2011) |
91
-| [KRAS](KRAS) | 1 | (Lohr et al. 2012) |
92
-| [LCOR](LCOR) | 1 | (Arthur et al. 2018) |
93
-| [LTB](LTB) | 1a | (Chapuy et al. 2018; Panea et al. 2019) |
94
-| [LYN](LYN) | 1 | (Chapuy et al. 2018) |
95
-| [MCL1](MCL1) | 1 | (Reddy et al. 2017; Panea et al. 2019) |
96
-| [MEF2B](MEF2B) | 1a | (Morin et al. 2011) |
97
-| [MEF2C](MEF2C) | 1a | (Arthur et al. 2018) |
98
-| [MGA](MGA) | 1 | (Zhang et al. 2013) |
99
-| [MPEG1](MPEG1) | 1 | (Morin et al. 2013) |
100
-| [MS4A1](MS4A1) | 1a | (Rushton et al. 2020) |
101
-| [MTOR](MTOR) | 1 | (Zhang et al. 2013; Panea et al. 2019) |
102
-| [MYC](MYC) | 1a | (Johnston and Carroll 1992; L. Pasqualucci et al. 2001) |
103
-| [MYD88](MYD88) | 1 | (Ngo et al. 2011) |
104
-| [MYOM2](MYOM2) | 1 | (Laura Pasqualucci, Trifonov, et al. 2011) |
105
-| [NCOR2](NCOR2) | 1 | (Schmitz et al. 2012) |
106
-| [NFKB1](NFKB1) | 1 | |
107
-| [NFKBIA](NFKBIA) | 1 | (Russler-Germain et al. 2023; Lake et al. 2009) |
108
-| [NFKBIE](NFKBIE) | 1 | (Morin et al. 2016) |
109
-| [NFKBIZ](NFKBIZ) | 1a | (Morin et al. 2016) |
110
-| [NLRC5](NLRC5) | 1 | |
111
-| [NOL9](NOL9) | 1 | (Schmitz et al. 2018) |
112
-| [NOTCH1](NOTCH1) | 1 | (Love et al. 2012; Laura Pasqualucci, Trifonov, et al. 2011) |
113
-| [NOTCH2](NOTCH2) | 1 | (Panea et al. 2019; Trøen et al. 2008) |
114
-| [OSBPL10](OSBPL10) | 1a | (Arthur et al. 2018) |
115
-| [P2RY8](P2RY8) | 1 | (Lohr et al. 2012; Muppidi et al. 2014) |
116
-| [PCBP1](PCBP1) | 1 | (Schmitz et al. 2012) |
117
-| [PIM1](PIM1) | 1a | (Burkhardt et al. 2022; L. Pasqualucci et al. 2001) |
118
-| [PIM2](PIM2) | 1a | (Arthur et al. 2018) |
119
-| [POU2AF1](POU2AF1) | 1a | (Krysiak et al. 2017) |
120
-| [POU2F2](POU2F2) | 1 | (Krysiak et al. 2017; Zhang et al. 2013) |
121
-| [PRDM1](PRDM1) | 1 | (Laura Pasqualucci et al. 2006) |
122
-| [PRKDC](PRKDC) | 1 | (Schmitz et al. 2018; Hübschmann et al. 2021) |
123
-| [PTEN](PTEN) | 1 | (Love et al. 2012) |
124
-| [PTPRD](PTPRD) | 1 | |
125
-| [RB1](RB1) | 1 | (Morin et al. 2013) |
126
-| [RFX7](RFX7) | 1 | (Grande et al. 2019) |
127
-| [RFXAP](RFXAP) | 1 | |
128
-| [RHOA](RHOA) | 1 | (Richter et al. 2012) |
129
-| [RRAGC](RRAGC) | 1 | (Okosun et al. 2016) |
130
-| [S1PR2](S1PR2) | 1a | (Muppidi et al. 2014; Morin et al. 2011) |
131
-| [SETD1B](SETD1B) | 1 | (Reddy et al. 2017) |
132
-| [SF3B1](SF3B1) | 1 | (Love et al. 2012) |
133
-| [SGK1](SGK1) | 1a | (Morin et al. 2011) |
134
-| [SIN3A](SIN3A) | 1 | (Grande et al. 2019) |
135
-| [SMARCA4](SMARCA4) | 1 | (Richter et al. 2012; Krysiak et al. 2017; Zhang et al. 2013) |
136
-| [SOCS1](SOCS1) | 1a | (Morin et al. 2011) |
137
-| [SPEN](SPEN) | 1 | (Rossi et al. 2012) |
138
-| [STAT3](STAT3) | 1 | (Ohgami et al. 2014) |
139
-| [STAT6](STAT6) | 1 | (Yildiz et al. 2015) |
140
-| [TAF1](TAF1) | 1 | (Morin et al. 2013) |
141
-| [TBL1XR1](TBL1XR1) | 1 | (Mareschal et al. 2016) |
142
-| [TET2](TET2) | 1 | (Albuquerque et al. 2017; Panea et al. 2019) |
143
-| [TMEM30A](TMEM30A) | 1 | (Morin et al. 2011) |
144
-| [TMSB4X](TMSB4X) | 1a | (Albuquerque et al. 2017) |
145
-| [TNFAIP3](TNFAIP3) | 1 | (Compagno et al. 2009) |
146
-| [TNFRSF14](TNFRSF14) | 1 | (Cheung et al. 2010) |
147
-| [TOX](TOX) | 1 | (Reddy et al. 2017) |
148
-| [TP53](TP53) | 1 | (Morin et al. 2011; Wilda et al. 2004) |
149
-| [TRIP12](TRIP12) | 1 | |
150
-| [TRRAP](TRRAP) | 1 | (Parry et al. 2013) |
151
-| [UBE2A](UBE2A) | 1 | (Reddy et al. 2017) |
152
-| [UNC5C](UNC5C) | 1 | |
153
-| [USP7](USP7) | 1 | (Grande et al. 2019) |
154
-| [VPS13B](VPS13B) | 1 | |
155
-| [WEE1](WEE1) | 1 | (Schmitz et al. 2018) |
156
-| [XPO1](XPO1) | 1 | (Mareschal et al. 2016) |
157
-| [ZC3H12A](ZC3H12A) | 1 | (Arthur et al. 2018) |
158
-| [ZFP36L1](ZFP36L1) | 1a | (Panea et al. 2019; Morin et al. 2011) |
159
-| [ZNF292](ZNF292) | 1 | (Zhang et al. 2013) |
160
-| [ZNF608](ZNF608) | 1 | (Krysiak et al. 2017; Zhang et al. 2013) |
161
-
162
-## Tier 2 DLBCL genes
163
-
164
-| Gene | Tier | Relevant references |
165
-|:----------------------:|:----:|:-----------------------------------------------------------:|
166
-| [ABI3BP](ABI3BP) | 2 | (Morin et al. 2013) |
167
-| [ADAMTS1](ADAMTS1) | 2 | (Hübschmann et al. 2021) |
168
-| [AICDA](AICDA) | 2a | (Arthur et al. 2018) |
169
-| [ANKRD12](ANKRD12) | 2 | (Hübschmann et al. 2021) |
170
-| [ANKRD17](ANKRD17) | 2 | (Reddy et al. 2017) |
171
-| [ARID1B](ARID1B) | 2 | (Reddy et al. 2017) |
172
-| [ARID5B](ARID5B) | 2 | (Reddy et al. 2017) |
173
-| [ATR](ATR) | 2 | (Reddy et al. 2017) |
174
-| [BIRC3](BIRC3) | 2a | (Arthur et al. 2018) |
175
-| [BLK](BLK) | 2a | |
176
-| [BRINP3](BRINP3) | 2 | (Reddy et al. 2017) |
177
-| [BTBD3](BTBD3) | 2 | (Reddy et al. 2017) |
178
-| [CADPS2](CADPS2) | 2 | (Hübschmann et al. 2021) |
179
-| [CBLB](CBLB) | 2 | (Reddy et al. 2017) |
180
-| [CCL4](CCL4) | 2 | (Chapuy et al. 2018) |
181
-| [CD22](CD22) | 2 | (Reddy et al. 2017) |
182
-| [CD44](CD44) | 2a | (Arthur et al. 2018) |
183
-| [CD74](CD74) | 2a | (Arthur et al. 2018) |
184
-| [CDC73](CDC73) | 2 | (Love et al. 2012; Reddy et al. 2017) |
185
-| [CDH9](CDH9) | 2 | (Morin et al. 2013) |
186
-| [CHD1](CHD1) | 2 | (Reddy et al. 2017) |
187
-| [CHD8](CHD8) | 2 | (Grande et al. 2019; Reddy et al. 2017) |
188
-| [CHST2](CHST2) | 2 | (Reddy et al. 2017) |
189
-| [CNOT2](CNOT2) | 2 | (Hübschmann et al. 2021) |
190
-| [CNTNAP5](CNTNAP5) | 2 | (Morin et al. 2013) |
191
-| [COQ7](COQ7) | 2 | (Chapuy et al. 2018) |
192
-| [CRIP1](CRIP1) | 2 | (Chapuy et al. 2018) |
193
-| [DCAF6](DCAF6) | 2 | (Reddy et al. 2017) |
194
-| [DDX10](DDX10) | 2 | (Reddy et al. 2017) |
195
-| [DHX16](DHX16) | 2 | (Hübschmann et al. 2021) |
196
-| [DICER1](DICER1) | 2 | (Reddy et al. 2017) |
197
-| [DNAH5](DNAH5) | 2 | (Morin et al. 2013) |
198
-| [DNM2](DNM2) | 2 | (Hübschmann et al. 2021) |
199
-| [DNMT3A](DNMT3A) | 2 | (Reddy et al. 2017) |
200
-| [DOCK1](DOCK1) | 2 | (Chapuy et al. 2018) |
201
-| [DSG4](DSG4) | 2 | (Morin et al. 2013) |
202
-| [EIF2AK3](EIF2AK3) | 2a | |
203
-| [EZR](EZR) | 2a | |
204
-| [FAM102A](FAM102A) | 2a | |
205
-| [FAM38B](FAM38B) | 2 | (Morin et al. 2013) |
206
-| [FANK1](FANK1) | 2a | |
207
-| [FAT4](FAT4) | 2 | (Morin et al. 2013) |
208
-| [FCRL3](FCRL3) | 2a | |
209
-| [FNBP1](FNBP1) | 2a | |
210
-| [FNDC1](FNDC1) | 2 | (Morin et al. 2013) |
211
-| [FOXP1](FOXP1) | 2a | (Reddy et al. 2017) |
212
-| [FUBP1](FUBP1) | 2 | (Reddy et al. 2017) |
213
-| [FUT5](FUT5) | 2 | (Chapuy et al. 2018) |
214
-| [GABRA2](GABRA2) | 2 | (Chapuy et al. 2018) |
215
-| [GAK](GAK) | 2 | (Hübschmann et al. 2021) |
216
-| [GNAS](GNAS) | 2 | (Reddy et al. 2017) |
217
-| [GOLGA5](GOLGA5) | 2 | (Reddy et al. 2017) |
218
-| [GPC5](GPC5) | 2 | (Schmitz et al. 2018) |
219
-| [GSG2](GSG2) | 2 | (Schmitz et al. 2018) |
220
-| [HDAC7](HDAC7) | 2 | (Morin et al. 2013) |
221
-| [HIST1H2AG](HIST1H2AG) | 2 | (Panea et al. 2019; Krysiak et al. 2017; Morin et al. 2013) |
222
-| [HNF1B](HNF1B) | 2 | (Laura Pasqualucci, Trifonov, et al. 2011) |
223
-| [HRAS](HRAS) | 2 | (Reddy et al. 2017) |
224
-| [ID3](ID3) | 2 | (Richter et al. 2012; Schmitz et al. 2012) |
225
-| [IER2](IER2) | 2 | (Morin et al. 2013) |
226
-| [IFNGR1](IFNGR1) | 2 | (Morin et al. 2013) |
227
-| [IGLL5](IGLL5) | 2a | (Panea et al. 2019; Russler-Germain et al. 2023) |
228
-| [IKBKB](IKBKB) | 2 | (Reddy et al. 2017) |
229
-| [IKBKE](IKBKE) | 2 | (Hübschmann et al. 2021) |
230
-| [IL6](IL6) | 2 | (Chapuy et al. 2018) |
231
-| [INO80](INO80) | 2 | (Zhang et al. 2013) |
232
-| [IRAG2](IRAG2) | 2a | |
233
-| [IRF1](IRF1) | 2a | (Hübschmann et al. 2021) |
234
-| [JAK1](JAK1) | 2 | (Zhang et al. 2013) |
235
-| [JAK3](JAK3) | 2 | (Zhang et al. 2013) |
236
-| [KCMF1](KCMF1) | 2 | (Reddy et al. 2017) |
237
-| [KLHL21](KLHL21) | 2 | (Schmitz et al. 2018) |
238
-| [LAMA5](LAMA5) | 2 | (Schmitz et al. 2018) |
239
-| [LAPTM5](LAPTM5) | 2a | (Hübschmann et al. 2021) |
240
-| [LIN54](LIN54) | 2 | (Reddy et al. 2017) |
241
-| [LPP](LPP) | 2a | (Arthur et al. 2018) |
242
-| [LRP12](LRP12) | 2 | (Hübschmann et al. 2021) |
243
-| [LRRN3](LRRN3) | 2 | (Morin et al. 2013) |
244
-| [MAGT1](MAGT1) | 2 | (Reddy et al. 2017) |
245
-| [MALAT1](MALAT1) | 2a | (Arthur et al. 2018) |
246
-| [MAP2K1](MAP2K1) | 2 | (Louissaint et al. 2016; Shin et al. 2015) |
247
-| [MAP4K4](MAP4K4) | 2 | (Reddy et al. 2017) |
248
-| [MARK1](MARK1) | 2 | (Reddy et al. 2017) |
249
-| [MECOM](MECOM) | 2 | (Reddy et al. 2017) |
250
-| [MET](MET) | 2 | (Reddy et al. 2017) |
251
-| [MIR142](MIR142) | 2a | (Kwanhian et al. 2012; Grande et al. 2019) |
252
-| [MIR155HG](MIR155HG) | 2a | |
253
-| [MPDZ](MPDZ) | 2 | (Morin et al. 2013) |
254
-| [MSH2](MSH2) | 2 | (Reddy et al. 2017) |
255
-| [MSH6](MSH6) | 2 | (Reddy et al. 2017) |
256
-| [MYB](MYB) | 2 | (Reddy et al. 2017) |
257
-| [MYBPC2](MYBPC2) | 2 | (Schmitz et al. 2018) |
258
-| [MYO1E](MYO1E) | 2a | |
259
-| [N2RF2](N2RF2) | 2 | (Hübschmann et al. 2021) |
260
-| [NANOG](NANOG) | 2 | (Chapuy et al. 2018) |
261
-| [NAV1](NAV1) | 2 | (Chapuy et al. 2018) |
262
-| [NCOA3](NCOA3) | 2a | |
263
-| [NCOR1](NCOR1) | 2 | (Reddy et al. 2017) |
264
-| [NEAT1](NEAT1) | 2a | (Arthur et al. 2018) |
265
-| [NF1](NF1) | 2 | (Reddy et al. 2017) |
266
-| [NFKB2](NFKB2) | 2 | (Reddy et al. 2017) |
267
-| [NLRP5](NLRP5) | 2 | (Morin et al. 2013) |
268
-| [NLRP8](NLRP8) | 2 | (Chapuy et al. 2018) |
269
-| [ODZ3](ODZ3) | 2 | (Morin et al. 2013) |
270
-| [P2RX5](P2RX5) | 2a | (Morin et al. 2013) |
271
-| [PAPOLG](PAPOLG) | 2 | (Schmitz et al. 2018) |
272
-| [PASK](PASK) | 2 | (Morin et al. 2013) |
273
-| [PAX5](PAX5) | 2a | (L. Pasqualucci et al. 2001) |
274
-| [PCDHB11](PCDHB11) | 2 | (Morin et al. 2013) |
275
-| [PCLO](PCLO) | 2 | (Lohr et al. 2012) |
276
-| [PDE4DIP](PDE4DIP) | 2 | (Chapuy et al. 2018) |
277
-| [PDS5B](PDS5B) | 2 | (Hübschmann et al. 2021; Morin et al. 2013) |
278
-| [PHF6](PHF6) | 2 | (Thomas et al. 2023; Reddy et al. 2017) |
279
-| [PIK3CD](PIK3CD) | 2 | (Reddy et al. 2017) |
280
-| [PIK3R1](PIK3R1) | 2 | (Zhang et al. 2013; Panea et al. 2019) |
281
-| [PKD1](PKD1) | 2 | (Morin et al. 2013) |
282
-| [PNPO](PNPO) | 2 | (Hübschmann et al. 2021) |
283
-| [POGZ](POGZ) | 2 | (Morin et al. 2013) |
284
-| [PPP1R9B](PPP1R9B) | 2 | |
285
-| [PRKCB](PRKCB) | 2 | (Morin et al. 2013) |
286
-| [PRPS1](PRPS1) | 2 | (Chapuy et al. 2018) |
287
-| [PTMA](PTMA) | 2a | |
288
-| [PTPN1](PTPN1) | 2a | |
289
-| [PTPN23](PTPN23) | 2 | (Morin et al. 2013) |
290
-| [PTPN6](PTPN6) | 2 | (Reddy et al. 2017) |
291
-| [PTPRK](PTPRK) | 2 | (Reddy et al. 2017) |
292
-| [RAC2](RAC2) | 2 | (Hübschmann et al. 2021; Panea et al. 2019) |
293
-| [RAD9A](RAD9A) | 2 | (Chapuy et al. 2018) |
294
-| [RARA](RARA) | 2 | (Reddy et al. 2017) |
295
-| [RCC](RCC) | 2a | |
296
-| [RFTN1](RFTN1) | 2a | (Arthur et al. 2018) |
297
-| [RHEX](RHEX) | 2a | |
298
-| [RHOH](RHOH) | 2a | (L. Pasqualucci et al. 2001) |
299
-| [RUBCNL](RUBCNL) | 2a | |
300
-| [RUNX1](RUNX1) | 2 | (Reddy et al. 2017) |
301
-| [SAMD9L](SAMD9L) | 2 | (Morin et al. 2013) |
302
-| [SARM1](SARM1) | 2 | (Morin et al. 2013) |
303
-| [SEL1L3](SEL1L3) | 2a | |
304
-| [SEPTIN9](SEPTIN9) | 2a | |
305
-| [SERPINA9](SERPINA9) | 2a | (Arthur et al. 2018) |
306
-| [SETD2](SETD2) | 2 | (Zhang et al. 2013) |
307
-| [SETD5](SETD5) | 2 | (Reddy et al. 2017) |
308
-| [SIAH2](SIAH2) | 2 | (Hübschmann et al. 2021) |
309
-| [SLC34A2](SLC34A2) | 2 | (Hübschmann et al. 2021) |
310
-| [SMEK1](SMEK1) | 2 | (Chapuy et al. 2018) |
311
-| [SRRM2](SRRM2) | 2 | (Russler-Germain et al. 2023; Morin et al. 2013) |
312
-| [ST6GAL1](ST6GAL1) | 2a | (Arthur et al. 2018) |
313
-| [STAT5B](STAT5B) | 2 | (Zhang et al. 2013) |
314
-| [SYK](SYK) | 2 | (Reddy et al. 2017) |
315
-| [SYPL1](SYPL1) | 2 | (Morin et al. 2013) |
316
-| [TAP1](TAP1) | 2 | (Schmitz et al. 2018) |
317
-| [TBC1D4](TBC1D4) | 2a | (Arthur et al. 2018) |
318
-| [TCL1A](TCL1A) | 2a | (Grande et al. 2019) |
319
-| [TGFBR2](TGFBR2) | 2 | (Reddy et al. 2017) |
320
-| [TIPARP](TIPARP) | 2 | (Reddy et al. 2017) |
321
-| [TLR2](TLR2) | 2 | (Chapuy et al. 2018) |
322
-| [TRAF3](TRAF3) | 2 | (Laura Pasqualucci, Trifonov, et al. 2011) |
323
-| [TRAF6](TRAF6) | 2 | (Hübschmann et al. 2021) |
324
-| [UBE2J1](UBE2J1) | 2a | |
325
-| [UBR5](UBR5) | 2 | (Zhang et al. 2013) |
326
-| [UNC5B](UNC5B) | 2 | (Hübschmann et al. 2021) |
327
-| [UNC5D](UNC5D) | 2 | |
328
-| [WAC](WAC) | 2 | (Reddy et al. 2017) |
329
-| [WDFY3](WDFY3) | 2 | (Morin et al. 2013) |
330
-| [WNK1](WNK1) | 2 | (Thomas et al. 2023; Hübschmann et al. 2021) |
331
-| [XBP1](XBP1) | 2a | |
332
-| [YY1](YY1) | 2 | (Reddy et al. 2017) |
333
-| [ZBTB7A](ZBTB7A) | 2 | (Reddy et al. 2017; Burkhardt et al. 2022) |
334
-| [ZCCHC7](ZCCHC7) | 2a | (Arthur et al. 2018) |
335
-| [ZEB2](ZEB2) | 2 | (Zhang et al. 2013) |
336
-| [ZFAT](ZFAT) | 2 | (Reddy et al. 2017) |
337
-| [ZFX](ZFX) | 2 | (Reddy et al. 2017) |
338
-| [ZNF217](ZNF217) | 2 | (Hübschmann et al. 2021) |
339
-| [ZNF423](ZNF423) | 2 | (Chapuy et al. 2018) |
340
-
341
-# References
342
-
343
-<div id="refs" class="references csl-bib-body hanging-indent">
344
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345
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346
-class="csl-entry">
347
-
348
-Albuquerque, Marco A., Bruno M. Grande, Elie J. Ritch, Prasath
349
-Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K. Grewal,
350
-Sohrab P. Shah, Paul C. Boutros, and Ryan D. Morin. 2017. “Enhancing
351
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352
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353
-
354
-</div>
355
-
356
-<div id="ref-arthurGenomewideDiscoverySomatic2018" class="csl-entry">
357
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805
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807
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811
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815
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824
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867
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FBXW7.pdf
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FIP1L1.md
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@@ -1,36 +0,0 @@
1
-# FIP1L1
2
-
3
-## Relevance tier by entity
4
-
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-
9
-## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10
-
11
-|Entity|source |frequency (%)|
12
-|:------:|:---------------------:|:-------------:|
13
-|BL |GAMBL genomes+capture|5.31 |
14
-|BL |Thomas cohort |2.50 |
15
-|BL |Panea cohort |2.00 |
16
-
17
-## Mutation pattern and selective pressure estimates
18
-
19
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
-|BL |No |Yes |1.128 |47.630 |
22
-|DLBCL |No |No |1.343 |10.476 |
23
-|FL |No |No |3.166 | 0.000 |
24
-
25
-
26
-
27
-View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/FIP1L1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/FIP1L1_protein_hg38.html)
28
-
29
-![image](images/proteinpaint/FIP1L1_NM_030917.svg)
30
-
31
-View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/FIP1L1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/FIP1L1_hg38.html)
32
-
33
-![image](images/proteinpaint/FIP1L1.svg)
34
-## FIP1L1 Expression
35
-![image](images/gene_expression/FIP1L1_by_pathology.svg)
36
-<!-- ORIGIN: Unknown -->
FL_genes_with_bib.md
... ...
@@ -1,561 +0,0 @@
1
-# FL genes
2
-
3
-## Origins of FL genes![sankey](FL_sankey-1.svg)
4
-
5
-## Tier 1 FL genes
6
-
7
-| Gene | Tier | Relevant references |
8
-|:----------------------:|:----:|:-------------------------------------------------------------------:|
9
-| [ACTB](ACTB) | 1a | (Lohr et al. 2012) |
10
-| [ARID1A](ARID1A) | 1 | (Love et al. 2012; Krysiak et al. 2017; Zhang et al. 2013) |
11
-| [ATP6AP1](ATP6AP1) | 1 | (Okosun et al. 2016) |
12
-| [ATP6V1B2](ATP6V1B2) | 1 | (Okosun et al. 2016) |
13
-| [B2M](B2M) | 1 | (Morin et al. 2011) |
14
-| [BCL2](BCL2) | 1a | (Tanaka et al. 1992; Burkhardt et al. 2022; Morin et al. 2011) |
15
-| [BCL6](BCL6) | 1a | (Morin et al. 2011; Love et al. 2012) |
16
-| [BCL7A](BCL7A) | 1a | (Arthur et al. 2018; Krysiak et al. 2017; Grande et al. 2019) |
17
-| [BIRC6](BIRC6) | 1 | (Reddy et al. 2017) |
18
-| [BTG1](BTG1) | 1a | (Morin et al. 2011; Burkhardt et al. 2022) |
19
-| [BTG2](BTG2) | 1a | (Love et al. 2012; Morin et al. 2011) |
20
-| [BTK](BTK) | 1 | (Krysiak et al. 2017; Albuquerque et al. 2017) |
21
-| [CARD11](CARD11) | 1 | (Lenz et al. 2008; Morin et al. 2011; Panea et al. 2019) |
22
-| [CCND3](CCND3) | 1 | (Morin et al. 2011; Richter et al. 2012) |
23
-| [CD83](CD83) | 1a | (Russler-Germain et al. 2023; Panea et al. 2019; Morin et al. 2013) |
24
-| [CREBBP](CREBBP) | 1 | (Laura Pasqualucci, Dominguez-Sola, et al. 2011; Love et al. 2012) |
25
-| [CTSS](CTSS) | 1 | (Bararia et al. 2020) |
26
-| [DTX1](DTX1) | 1a | (Panea et al. 2019; Schmitz et al. 2018) |
27
-| [EBF1](EBF1) | 1a | (Thomas et al. 2023; Bohle et al. 2013) |
28
-| [EEF1A1](EEF1A1) | 1 | (Hübschmann et al. 2021) |
29
-| [EP300](EP300) | 1 | (Laura Pasqualucci, Dominguez-Sola, et al. 2011; Panea et al. 2019) |
30
-| [EZH2](EZH2) | 1 | (Morin et al. 2010; Love et al. 2012) |
31
-| [FAS](FAS) | 1 | (Scholl et al. 2007) |
32
-| [FOXO1](FOXO1) | 1 | (Morin et al. 2011; Schmitz et al. 2012) |
33
-| [GNA13](GNA13) | 1 | (Morin et al. 2011; Love et al. 2012) |
34
-| [GNAI2](GNAI2) | 1 | (Morin et al. 2013; Grande et al. 2019) |
35
-| [HIST1H1B](HIST1H1B) | 1a | (Krysiak et al. 2017; Chapuy et al. 2018) |
36
-| [HIST1H1C](HIST1H1C) | 1a | (Morin et al. 2011; Panea et al. 2019) |
37
-| [HIST1H1D](HIST1H1D) | 1a | (Morin et al. 2013; Krysiak et al. 2017) |
38
-| [HIST1H1E](HIST1H1E) | 1a | (Grande et al. 2019; Morin et al. 2013; Krysiak et al. 2017) |
39
-| [HIST1H2AC](HIST1H2AC) | 1a | (Morin et al. 2013; Krysiak et al. 2017) |
40
-| [HIST1H2AG](HIST1H2AG) | 1a | (Panea et al. 2019; Morin et al. 2013; Krysiak et al. 2017) |
41
-| [HIST1H2AM](HIST1H2AM) | 1a | (Krysiak et al. 2017; Panea et al. 2019) |
42
-| [HIST1H2BC](HIST1H2BC) | 1a | (Reddy et al. 2017; Krysiak et al. 2017) |
43
-| [HIST1H2BD](HIST1H2BD) | 1a | (Krysiak et al. 2017) |
44
-| [HIST1H2BG](HIST1H2BG) | 1a | (Krysiak et al. 2017) |
45
-| [HIST1H3B](HIST1H3B) | 1a | (Zhang et al. 2013) |
46
-| [HIST1H3G](HIST1H3G) | 1a | (Krysiak et al. 2017) |
47
-| [HVCN1](HVCN1) | 1 | (Krysiak et al. 2017) |
48
-| [IRF4](IRF4) | 1a | (Morin et al. 2011) |
49
-| [IRF8](IRF8) | 1a | (Panea et al. 2019; Morin et al. 2011) |
50
-| [ITPKB](ITPKB) | 1 | (Schmitz et al. 2018) |
51
-| [KLF2](KLF2) | 1a | (Laura Pasqualucci, Trifonov, et al. 2011) |
52
-| [KLHL6](KLHL6) | 1a | (Panea et al. 2019; Morin et al. 2011) |
53
-| [KMT2D](KMT2D) | 1 | (Morin et al. 2011; Grande et al. 2019) |
54
-| [LTB](LTB) | 1a | (Panea et al. 2019; Chapuy et al. 2018) |
55
-| [MAP2K1](MAP2K1) | 1 | (Shin et al. 2015; Louissaint et al. 2016) |
56
-| [MEF2B](MEF2B) | 1a | (Morin et al. 2011) |
57
-| [MEF2C](MEF2C) | 1a | (Arthur et al. 2018) |
58
-| [PCLO](PCLO) | 1 | (Lohr et al. 2012) |
59
-| [PIM1](PIM1) | 1a | (L. Pasqualucci et al. 2001; Burkhardt et al. 2022) |
60
-| [POU2AF1](POU2AF1) | 1 | (Krysiak et al. 2017) |
61
-| [POU2F2](POU2F2) | 1 | (Krysiak et al. 2017; Zhang et al. 2013) |
62
-| [PTPRD](PTPRD) | 1 | |
63
-| [RRAGC](RRAGC) | 1 | (Okosun et al. 2016) |
64
-| [S1PR2](S1PR2) | 1a | (Morin et al. 2011; Muppidi et al. 2014) |
65
-| [SGK1](SGK1) | 1a | (Morin et al. 2011) |
66
-| [SMARCA4](SMARCA4) | 1 | (Zhang et al. 2013; Krysiak et al. 2017; Richter et al. 2012) |
67
-| [SOCS1](SOCS1) | 1a | (Morin et al. 2011) |
68
-| [STAT6](STAT6) | 1 | (Yildiz et al. 2015) |
69
-| [TBL1XR1](TBL1XR1) | 1 | (Mareschal et al. 2016) |
70
-| [TMSB4X](TMSB4X) | 1a | (Albuquerque et al. 2017) |
71
-| [TNFAIP3](TNFAIP3) | 1 | (Compagno et al. 2009) |
72
-| [TNFRSF14](TNFRSF14) | 1 | (Cheung et al. 2010) |
73
-| [TP53](TP53) | 1 | (Wilda et al. 2004; Morin et al. 2011) |
74
-| [VMA21](VMA21) | 1 | (Hübschmann et al. 2021) |
75
-
76
-## Tier 2 FL genes
77
-
78
-| Gene | Tier | Relevant references |
79
-|:----------------------:|:----:|:------------------------------------------------------------------:|
80
-| [ABL2](ABL2) | 2 | (Russler-Germain et al. 2023) |
81
-| [ACTG1](ACTG1) | 2a | (Hübschmann et al. 2021) |
82
-| [ATP6V1A](ATP6V1A) | 2 | (Hübschmann et al. 2021) |
83
-| [BCL10](BCL10) | 2 | (Russler-Germain et al. 2023; Morin et al. 2011) |
84
-| [CCDC42BPB](CCDC42BPB) | 2 | (Hübschmann et al. 2021) |
85
-| [CD70](CD70) | 2 | (Morin et al. 2011; Russler-Germain et al. 2023) |
86
-| [CD79B](CD79B) | 2 | (Morin et al. 2011; Panea et al. 2019) |
87
-| [CILP](CILP) | 2 | (Russler-Germain et al. 2023) |
88
-| [CPNE8](CPNE8) | 2 | (Hübschmann et al. 2021) |
89
-| [CXCR4](CXCR4) | 2a | (Khodabakhshi et al. 2012; Panea et al. 2019; Krysiak et al. 2017) |
90
-| [CYP2A6](CYP2A6) | 2 | (Russler-Germain et al. 2023) |
91
-| [DDX3X](DDX3X) | 2 | (Schmitz et al. 2012, 2018) |
92
-| [DHX15](DHX15) | 2 | (Hübschmann et al. 2021) |
93
-| [DUSP2](DUSP2) | 2a | (Morin et al. 2013) |
94
-| [EGR1](EGR1) | 2 | (Krysiak et al. 2017) |
95
-| [FZR1](FZR1) | 2 | (Hübschmann et al. 2021) |
96
-| [GBP7](GBP7) | 2 | (Russler-Germain et al. 2023) |
97
-| [GRM6](GRM6) | 2 | (Russler-Germain et al. 2023) |
98
-| [HIST1H2BM](HIST1H2BM) | 2a | (Krysiak et al. 2017) |
99
-| [HIST1H3I](HIST1H3I) | 2a | (Krysiak et al. 2017; Panea et al. 2019) |
100
-| [HLA-B](HLA-B) | 2 | |
101
-| [HNRNPD](HNRNPD) | 2 | |
102
-| [IGLL5](IGLL5) | 2a | (Panea et al. 2019; Russler-Germain et al. 2023) |
103
-| [JUP](JUP) | 2 | (Hübschmann et al. 2021) |
104
-| [KIR3DL1](KIR3DL1) | 2 | (Russler-Germain et al. 2023) |
105
-| [LAPTM5](LAPTM5) | 2 | (Hübschmann et al. 2021) |
106
-| [MAGEC1](MAGEC1) | 2 | (Russler-Germain et al. 2023) |
107
-| [MAP7D1](MAP7D1) | 2 | (Russler-Germain et al. 2023) |
108
-| [MGEA5](MGEA5) | 2 | (Hübschmann et al. 2021) |
109
-| [MKI67](MKI67) | 2 | (Russler-Germain et al. 2023; Schmitz et al. 2012) |
110
-| [MYC](MYC) | 2a | (L. Pasqualucci et al. 2001; Johnston and Carroll 1992) |
111
-| [MYCBP2](MYCBP2) | 2 | (Hübschmann et al. 2021) |
112
-| [MYD88](MYD88) | 2 | (Ngo et al. 2011) |
113
-| [NFKBIA](NFKBIA) | 2 | (Russler-Germain et al. 2023; Lake et al. 2009) |
114
-| [OR8H2](OR8H2) | 2 | (Russler-Germain et al. 2023) |
115
-| [P2RY8](P2RY8) | 2 | (Muppidi et al. 2014; Lohr et al. 2012) |
116
-| [PDS5B](PDS5B) | 2 | (Hübschmann et al. 2021; Morin et al. 2013) |
117
-| [PPP4C](PPP4C) | 2 | (Hübschmann et al. 2021) |
118
-| [PRKDC](PRKDC) | 2 | (Schmitz et al. 2018; Hübschmann et al. 2021) |
119
-| [PZP](PZP) | 2 | (Russler-Germain et al. 2023) |
120
-| [RBM6](RBM6) | 2 | (Hübschmann et al. 2021) |
121
-| [SESN1](SESN1) | 2 | (Oricchio et al. 2017) |
122
-| [SHROOM3](SHROOM3) | 2 | (Russler-Germain et al. 2023) |
123
-| [SRRM2](SRRM2) | 2 | (Morin et al. 2013; Russler-Germain et al. 2023) |
124
-| [STAB2](STAB2) | 2 | (Russler-Germain et al. 2023) |
125
-| [TMEM30A](TMEM30A) | 2 | (Morin et al. 2011) |
126
-| [TPP1](TPP1) | 2 | (Hübschmann et al. 2021) |
127
-| [XIRP2](XIRP2) | 2 | (Russler-Germain et al. 2023) |
128
-| [ZC3H12A](ZC3H12A) | 2 | (Arthur et al. 2018) |
129
-| [ZNF608](ZNF608) | 2 | (Krysiak et al. 2017; Zhang et al. 2013) |
130
-
131
-# References
132
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133
-<div id="refs" class="references csl-bib-body hanging-indent">
134
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183
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193
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203
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HNRNPU.pdf
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PRKCD.md
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-# PRKCD
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-
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-## Relevance tier by entity
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-
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-|Entity|Tier|Description |
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-|:------:|:----:|--------------------------------------|
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-|BL |2 |relevance in BL not firmly established|
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-
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-## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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-
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-|Entity|source |frequency (%)|
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-|:------:|:---------------------:|:-------------:|
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-|BL |GAMBL genomes+capture|2.31 |
14
-|BL |Thomas cohort |1.30 |
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-|BL |Panea cohort |5.90 |
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-
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-## Mutation pattern and selective pressure estimates
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-
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-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
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-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
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-|BL |No |No | 2.225 | 0.000 |
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-|DLBCL |No |Yes |11.290 |71.966 |
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-|FL |No |No |25.696 | 0.000 |
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-
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-
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-
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-View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRKCD_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRKCD_protein_hg38.html)
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-
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-![image](images/proteinpaint/PRKCD_NM_006254.svg)
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-
31
-View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRKCD.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRKCD_hg38.html)
32
-
33
-![image](images/proteinpaint/PRKCD.svg)
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-## PRKCD Expression
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-![image](images/gene_expression/PRKCD_by_pathology.svg)
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-<!-- ORIGIN: Unknown -->
RARA.pdf
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RCC.md
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-# RCC
2
-
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-## Relevance tier by entity
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-
5
-|Entity|Tier|Description |
6
-|:------:|:----:|-----------------------------------------|
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-|DLBCL |2 |relevance in DLBCL not firmly established|
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-
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-## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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-
11
-|Entity|source |frequency (%)|
12
-|:------:|:--------------:|:-------------:|
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-|DLBCL |GAMBL genomes |NA |
14
-|DLBCL |Schmitz cohort|NA |
15
-|DLBCL |Reddy cohort |NA |
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-|DLBCL |Chapuy cohort |NA |
17
-
18
-## Mutation pattern and selective pressure estimates
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-
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-|
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-
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-## RCC Expression
23
-![image](images/gene_expression/RCC_by_pathology.svg)
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-<h1 id="tgfbr2">TGFBR2</h1>
369
-<h2 id="history">History</h2>
370
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
-timeline
372
- title Publication timing
373
- 2017-10-10 : Reddy : DLBCL
374
-</div></code></pre>
375
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
376
-<table>
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-<thead>
378
-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">Tier</th>
381
-<th>Description</th>
382
-</tr>
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-</thead>
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-<tbody>
385
-<tr>
386
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
387
-<td style="text-align:center">2</td>
388
-<td>relevance in DLBCL not firmly established</td>
389
-</tr>
390
-</tbody>
391
-</table>
392
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
393
-<table>
394
-<thead>
395
-<tr>
396
-<th style="text-align:center">Entity</th>
397
-<th style="text-align:center">source</th>
398
-<th style="text-align:center">frequency (%)</th>
399
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-<td style="text-align:center">DLBCL</td>
404
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405
-<td style="text-align:center">2.10</td>
406
-</tr>
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408
-<td style="text-align:center">DLBCL</td>
409
-<td style="text-align:center">Schmitz cohort</td>
410
-<td style="text-align:center">1.91</td>
411
-</tr>
412
-<tr>
413
-<td style="text-align:center">DLBCL</td>
414
-<td style="text-align:center">Reddy cohort</td>
415
-<td style="text-align:center">1.90</td>
416
-</tr>
417
-<tr>
418
-<td style="text-align:center">DLBCL</td>
419
-<td style="text-align:center">Chapuy cohort</td>
420
-<td style="text-align:center">1.28</td>
421
-</tr>
422
-</tbody>
423
-</table>
424
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
425
-<table>
426
-<thead>
427
-<tr>
428
-<th style="text-align:center">Entity</th>
429
-<th style="text-align:center">aSHM</th>
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-<th style="text-align:center">dN/dS (missense)</th>
432
-<th style="text-align:center">dN/dS (nonsense)</th>
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-</tr>
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-</thead>
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-<tbody>
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-<tr>
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-<td style="text-align:center">BL</td>
438
-<td style="text-align:center">No</td>
439
-<td style="text-align:center">No</td>
440
-<td style="text-align:center">0.941</td>
441
-<td style="text-align:center">0.000</td>
442
-</tr>
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-<tr>
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-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">No</td>
446
-<td style="text-align:center">No</td>
447
-<td style="text-align:center">0.599</td>
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-<td style="text-align:center">8.085</td>
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-<td style="text-align:center">FL</td>
452
-<td style="text-align:center">No</td>
453
-<td style="text-align:center">No</td>
454
-<td style="text-align:center">2.530</td>
455
-<td style="text-align:center">0.000</td>
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-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/TGFBR2_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/TGFBR2_protein_hg38.html">hg38</a></p>
460
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/TGFBR2_NM_001024847.svg" alt="image"></p>
461
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/TGFBR2.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/TGFBR2_hg38.html">hg38</a></p>
462
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/TGFBR2.svg" alt="image"></p>
463
-<h2 id="tgfbr2-expression">TGFBR2 Expression</h2>
464
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/TGFBR2_by_pathology.svg" alt="image"></p>
465
-<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
466
-<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
467
-<h2 id="references">References</h2>
468
-<ol>
469
-<li>Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.</li>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">Tier</th>
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-<tbody>
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-<td style="text-align:center">1</td>
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-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/UNC5C_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/UNC5C_protein_hg38.html">hg38</a></p>
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351
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352
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- ? 'dark'
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- });
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- </script>
368
-<h1 id="zfx">ZFX</h1>
369
-<h2 id="history">History</h2>
370
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
-timeline
372
- title Publication timing
373
- 2017-10-10 : Reddy : DLBCL
374
-</div></code></pre>
375
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
376
-<table>
377
-<thead>
378
-<tr>
379
-<th style="text-align:center">Entity</th>
380
-<th style="text-align:center">Tier</th>
381
-<th>Description</th>
382
-</tr>
383
-</thead>
384
-<tbody>
385
-<tr>
386
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
387
-<td style="text-align:center">2</td>
388
-<td>relevance in DLBCL not firmly established</td>
389
-</tr>
390
-</tbody>
391
-</table>
392
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
393
-<table>
394
-<thead>
395
-<tr>
396
-<th style="text-align:center">Entity</th>
397
-<th style="text-align:center">source</th>
398
-<th style="text-align:center">frequency (%)</th>
399
-</tr>
400
-</thead>
401
-<tbody>
402
-<tr>
403
-<td style="text-align:center">DLBCL</td>
404
-<td style="text-align:center">GAMBL genomes</td>
405
-<td style="text-align:center">0.38</td>
406
-</tr>
407
-<tr>
408
-<td style="text-align:center">DLBCL</td>
409
-<td style="text-align:center">Schmitz cohort</td>
410
-<td style="text-align:center">1.70</td>
411
-</tr>
412
-<tr>
413
-<td style="text-align:center">DLBCL</td>
414
-<td style="text-align:center">Reddy cohort</td>
415
-<td style="text-align:center">1.40</td>
416
-</tr>
417
-<tr>
418
-<td style="text-align:center">DLBCL</td>
419
-<td style="text-align:center">Chapuy cohort</td>
420
-<td style="text-align:center">0.43</td>
421
-</tr>
422
-</tbody>
423
-</table>
424
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
425
-<table>
426
-<thead>
427
-<tr>
428
-<th style="text-align:center">Entity</th>
429
-<th style="text-align:center">aSHM</th>
430
-<th style="text-align:center">Significant selection</th>
431
-<th style="text-align:center">dN/dS (missense)</th>
432
-<th style="text-align:center">dN/dS (nonsense)</th>
433
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-</thead>
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-<tbody>
436
-<tr>
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-<td style="text-align:center">BL</td>
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-<td style="text-align:center">No</td>
439
-<td style="text-align:center">No</td>
440
-<td style="text-align:center">3.677</td>
441
-<td style="text-align:center">0</td>
442
-</tr>
443
-<tr>
444
-<td style="text-align:center">DLBCL</td>
445
-<td style="text-align:center">No</td>
446
-<td style="text-align:center">No</td>
447
-<td style="text-align:center">0.000</td>
448
-<td style="text-align:center">0</td>
449
-</tr>
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-<tr>
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-<td style="text-align:center">FL</td>
452
-<td style="text-align:center">No</td>
453
-<td style="text-align:center">No</td>
454
-<td style="text-align:center">0.000</td>
455
-<td style="text-align:center">0</td>
456
-</tr>
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-</tbody>
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-</table>
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-<blockquote>
460
-<p>[!NOTE]
461
-First described in DLBCL in 2017 by <a href="https://pubmed.ncbi.nlm.nih.gov/28985567">Reddy A</a></p>
462
-</blockquote>
463
-<blockquote>
464
-<p>[!WARNING]
465
-Mutations in this gene were reported to be inflated in the original results according to <a href="https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1">Dreval K</a></p>
466
-</blockquote>
467
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ZFX_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ZFX_protein_hg38.html">hg38</a></p>
468
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ZFX_NM_003410.svg" alt="image"></p>
469
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ZFX.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ZFX_hg38.html">hg38</a></p>
470
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ZFX.svg" alt="image"></p>
471
-<h2 id="zfx-expression">ZFX Expression</h2>
472
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/ZFX_by_pathology.svg" alt="image"></p>
473
-<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
474
-<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
475
-<h2 id="references">References</h2>
476
-<ol>
477
-<li>Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.</li>
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370
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
-timeline
372
- title Publication timing
373
- 2018-05-01 : Chapuy : DLBCL
374
-</div></code></pre>
375
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
376
-<table>
377
-<thead>
378
-<tr>
379
-<th style="text-align:center">Entity</th>
380
-<th style="text-align:center">Tier</th>
381
-<th>Description</th>
382
-</tr>
383
-</thead>
384
-<tbody>
385
-<tr>
386
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
387
-<td style="text-align:center">2</td>
388
-<td>relevance in DLBCL not firmly established</td>
389
-</tr>
390
-</tbody>
391
-</table>
392
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
393
-<table>
394
-<thead>
395
-<tr>
396
-<th style="text-align:center">Entity</th>
397
-<th style="text-align:center">source</th>
398
-<th style="text-align:center">frequency (%)</th>
399
-</tr>
400
-</thead>
401
-<tbody>
402
-<tr>
403
-<td style="text-align:center">DLBCL</td>
404
-<td style="text-align:center">GAMBL genomes</td>
405
-<td style="text-align:center">1.91</td>
406
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407
-<tr>
408
-<td style="text-align:center">DLBCL</td>
409
-<td style="text-align:center">Schmitz cohort</td>
410
-<td style="text-align:center">3.40</td>
411
-</tr>
412
-<tr>
413
-<td style="text-align:center">DLBCL</td>
414
-<td style="text-align:center">Reddy cohort</td>
415
-<td style="text-align:center">2.10</td>
416
-</tr>
417
-<tr>
418
-<td style="text-align:center">DLBCL</td>
419
-<td style="text-align:center">Chapuy cohort</td>
420
-<td style="text-align:center">3.42</td>
421
-</tr>
422
-</tbody>
423
-</table>
424
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
425
-<table>
426
-<thead>
427
-<tr>
428
-<th style="text-align:center">Entity</th>
429
-<th style="text-align:center">aSHM</th>
430
-<th style="text-align:center">Significant selection</th>
431
-<th style="text-align:center">dN/dS (missense)</th>
432
-<th style="text-align:center">dN/dS (nonsense)</th>
433
-</tr>
434
-</thead>
435
-<tbody>
436
-<tr>
437
-<td style="text-align:center">BL</td>
438
-<td style="text-align:center">No</td>
439
-<td style="text-align:center">No</td>
440
-<td style="text-align:center">0.594</td>
441
-<td style="text-align:center">0</td>
442
-</tr>
443
-<tr>
444
-<td style="text-align:center">DLBCL</td>
445
-<td style="text-align:center">No</td>
446
-<td style="text-align:center">No</td>
447
-<td style="text-align:center">1.430</td>
448
-<td style="text-align:center">0</td>
449
-</tr>
450
-<tr>
451
-<td style="text-align:center">FL</td>
452
-<td style="text-align:center">No</td>
453
-<td style="text-align:center">No</td>
454
-<td style="text-align:center">0.836</td>
455
-<td style="text-align:center">0</td>
456
-</tr>
457
-</tbody>
458
-</table>
459
-<blockquote>
460
-<p>[!NOTE]
461
-First described in DLBCL in 2018 by <a href="https://pubmed.ncbi.nlm.nih.gov/29713087">Chapuy B</a></p>
462
-</blockquote>
463
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423_protein_hg38.html">hg38</a></p>
464
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ZNF423_NM_015069.svg" alt="image"></p>
465
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423_hg38.html">hg38</a></p>
466
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ZNF423.svg" alt="image"></p>
467
-<h2 id="znf423-expression">ZNF423 Expression</h2>
468
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/ZNF423_by_pathology.svg" alt="image"></p>
469
-<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
470
-<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
471
-<h2 id="references">References</h2>
472
-<ol>
473
-<li>Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387</li>
474
-</ol>
475
-
476
-</body>
477
-</html>
abateDistinctViralMutational2015a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @abateDistinctViralMutational2015a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL||1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1,
26
-This study, BL Tier 2, 1
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[CCNF](CCNF)|2 |
37
-
38
-# Details
39
-
albuquerqueEnhancingKnowledgeDiscovery2017a.md
... ...
@@ -1,41 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @albuquerqueEnhancingKnowledgeDiscovery2017a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 3
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[BTK](BTK)|1 |
37
-|[TET2](TET2)|1 |
38
-|[TMSB4X](TMSB4X)|1 |
39
-
40
-# Details
41
-
arthurGenomewideDiscoverySomatic2018.md
... ...
@@ -1,58 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @arthurGenomewideDiscoverySomatic2018
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|8|12|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 8
26
-This study, DLBCL Tier 2, 12
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[AICDA](AICDA)|2 |
37
-|[BCL7A](BCL7A)|1 |
38
-|[BIRC3](BIRC3)|2 |
39
-|[CD44](CD44)|2 |
40
-|[CD74](CD74)|2 |
41
-|[ETV6](ETV6)|1 |
42
-|[GRHPR](GRHPR)|1 |
43
-|[LCOR](LCOR)|1 |
44
-|[LPP](LPP)|2 |
45
-|[MALAT1](MALAT1)|2 |
46
-|[MEF2C](MEF2C)|1 |
47
-|[NEAT1](NEAT1)|2 |
48
-|[OSBPL10](OSBPL10)|1 |
49
-|[PIM2](PIM2)|1 |
50
-|[RFTN1](RFTN1)|2 |
51
-|[SERPINA9](SERPINA9)|2 |
52
-|[ST6GAL1](ST6GAL1)|2 |
53
-|[TBC1D4](TBC1D4)|2 |
54
-|[ZC3H12A](ZC3H12A)|1 |
55
-|[ZCCHC7](ZCCHC7)|2 |
56
-
57
-# Details
58
-
barariaCathepsinAlterationsInduce2020c.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @barariaCathepsinAlterationsInduce2020c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, FL Tier 1, 1
26
-This study, FL Tier 2,
27
-Other FL studies, FL Tier 1, 66
28
-Other FL studies, FL Tier 2, 50
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|FL tier|
35
-|:-|:-:|
36
-|[CTSS](CTSS)|1 |
37
-
38
-# Details
39
-
beaLandscapeSomaticMutations2013.md
... ...
@@ -1,65 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @beaLandscapeSomaticMutations2013
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|11|16|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MCL Tier 1, 11
26
-This study, MCL Tier 2, 16
27
-Other MCL studies, MCL Tier 1, 23
28
-Other MCL studies, MCL Tier 2, 46
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MCL tier|
35
-|:-|:-:|
36
-|[ABCA3](ABCA3)|2 |
37
-|[ABCC9](ABCC9)|2 |
38
-|[ATM](ATM)|1 |
39
-|[BIRC3](BIRC3)|1 |
40
-|[CCND1](CCND1)|1 |
41
-|[CHMP4C](CHMP4C)|2 |
42
-|[CRYBG3](CRYBG3)|2 |
43
-|[DCP1B](DCP1B)|2 |
44
-|[DLGAP2](DLGAP2)|2 |
45
-|[DNAJC6](DNAJC6)|2 |
46
-|[KCNC2](KCNC2)|2 |
47
-|[KIAA1671](KIAA1671)|2 |
48
-|[KMT2D](KMT2D)|1 |
49
-|[LUZP4](LUZP4)|2 |
50
-|[MEF2B](MEF2B)|1 |
51
-|[NOTCH1](NOTCH1)|1 |
52
-|[NOTCH2](NOTCH2)|1 |
53
-|[NSD2](NSD2)|1 |
54
-|[PCSK2](PCSK2)|2 |
55
-|[PDLIM3](PDLIM3)|2 |
56
-|[RGS4](RGS4)|2 |
57
-|[SLC17A6](SLC17A6)|2 |
58
-|[SP140](SP140)|1 |
59
-|[TLR2](TLR2)|1 |
60
-|[TNRC6B](TNRC6B)|2 |
61
-|[TP53](TP53)|1 |
62
-|[TRPM6](TRPM6)|2 |
63
-
64
-# Details
65
-
bohleRoleEarlyBcell2013.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @bohleRoleEarlyBcell2013
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[EBF1](EBF1)|1 |
37
-
38
-# Details
39
-
braggioGenomicAnalysisMarginal2012.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @braggioGenomicAnalysisMarginal2012
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MZL Tier 1, 1
26
-This study, MZL Tier 2,
27
-Other MZL studies, MZL Tier 1, 42
28
-Other MZL studies, MZL Tier 2, 74
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MZL tier|
35
-|:-|:-:|
36
-|[ATM](ATM)|1 |
37
-
38
-# Details
39
-
burkhardtClinicalRelevanceMolecular2022b.md
... ...
@@ -1,63 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @burkhardtClinicalRelevanceMolecular2022b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL||25|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1,
26
-This study, BL Tier 2, 25
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[ADAMTS5](ADAMTS5)|2 |
37
-|[ADNP](ADNP)|2 |
38
-|[AGO4](AGO4)|2 |
39
-|[BCL2](BCL2)|2 |
40
-|[BTG1](BTG1)|2 |
41
-|[CD79A](CD79A)|2 |
42
-|[CHD4](CHD4)|2 |
43
-|[CPXM2](CPXM2)|2 |
44
-|[E2F2](E2F2)|2 |
45
-|[EDNRB](EDNRB)|2 |
46
-|[ERAP1](ERAP1)|2 |
47
-|[HLA-DQB1](HLA-DQB1)|2 |
48
-|[KLHL26](KLHL26)|2 |
49
-|[NOA1](NOA1)|2 |
50
-|[PIM1](PIM1)|2 |
51
-|[PPP6R2](PPP6R2)|2 |
52
-|[PREX1](PREX1)|2 |
53
-|[REV3L](REV3L)|2 |
54
-|[RPL10](RPL10)|2 |
55
-|[SAL3](SAL3)|2 |
56
-|[TTN](TTN)|2 |
57
-|[VWA7](VWA7)|2 |
58
-|[ZAN](ZAN)|2 |
59
-|[ZBTB7A](ZBTB7A)|2 |
60
-|[ZNF85](ZNF85)|2 |
61
-
62
-# Details
63
-
chapuyMolecularSubtypesDiffuse2018b.md
... ...
@@ -1,57 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @chapuyMolecularSubtypesDiffuse2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|17|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 2
26
-This study, DLBCL Tier 2, 17
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[CCL4](CCL4)|2 |
37
-|[COQ7](COQ7)|2 |
38
-|[CRIP1](CRIP1)|2 |
39
-|[DOCK1](DOCK1)|2 |
40
-|[FUT5](FUT5)|2 |
41
-|[GABRA2](GABRA2)|2 |
42
-|[HIST1H1B](HIST1H1B)|1 |
43
-|[IL6](IL6)|2 |
44
-|[LTB](LTB)|1 |
45
-|[LYN](LYN)|2 |
46
-|[NANOG](NANOG)|2 |
47
-|[NAV1](NAV1)|2 |
48
-|[NLRP8](NLRP8)|2 |
49
-|[PDE4DIP](PDE4DIP)|2 |
50
-|[PRPS1](PRPS1)|2 |
51
-|[RAD9A](RAD9A)|2 |
52
-|[SMEK1](SMEK1)|2 |
53
-|[TLR2](TLR2)|2 |
54
-|[ZNF423](ZNF423)|2 |
55
-
56
-# Details
57
-
cheungAcquiredTNFRSF14Mutations2010a.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @cheungAcquiredTNFRSF14Mutations2010a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-|FL|1||
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, DLBCL Tier 1, 1
27
-This study, DLBCL Tier 2,
28
-Other DLBCL studies, DLBCL Tier 1, 128
29
-Other DLBCL studies, DLBCL Tier 2, 198
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|DLBCL tier|FL tier|
36
-|:-|:-:|:-:|
37
-|[TNFRSF14](TNFRSF14)|1 |1 |
38
-
39
-# Details
40
-
compagnoMutationsMultipleGenes2009a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @compagnoMutationsMultipleGenes2009a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[TNFAIP3](TNFAIP3)|1 |
37
-
38
-# Details
39
-
deschGenotypingCirculatingTumor2020.md
... ...
@@ -1,48 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @deschGenotypingCirculatingTumor2020
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|9|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2, 9
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[ACTG1](ACTG1)|2 |
37
-|[CCND3](CCND3)|2 |
38
-|[CDH2](CDH2)|2 |
39
-|[EZR](EZR)|2 |
40
-|[HLA-A](HLA-A)|2 |
41
-|[IGLL5](IGLL5)|2 |
42
-|[KLF2](KLF2)|2 |
43
-|[KMT2D](KMT2D)|2 |
44
-|[LTB](LTB)|1 |
45
-|[MYB](MYB)|2 |
46
-
47
-# Details
48
-
dunsCharacterizationDLBCLPMBL2021b.md
... ...
@@ -1,53 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @dunsCharacterizationDLBCLPMBL2021b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|8|3|
12
-|PMBL|6|8|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, PMBL Tier 1, 6
27
-This study, PMBL Tier 2, 8
28
-Other PMBL studies, PMBL Tier 1, 76
29
-Other PMBL studies, PMBL Tier 2, 82
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|DLBCL tier|PMBL tier|
36
-|:-|:-:|:-:|
37
-|[BIRC3](BIRC3)|2 |2 |
38
-|[CD83](CD83)|1 |1 |
39
-|[CREBBP](CREBBP)|1 |1 |
40
-|[DUSP2](DUSP2)|1 |1 |
41
-|[FOXO1](FOXO1)|1 |2 |
42
-|[HRNR](HRNR)| |2 |
43
-|[IL4R](IL4R)|1 |1 |
44
-|[LPHN3](LPHN3)| |2 |
45
-|[MCL1](MCL1)|2 |2 |
46
-|[MYC](MYC)|1 |2 |
47
-|[PIM1](PIM1)|1 |1 |
48
-|[RFTN1](RFTN1)|2 |2 |
49
-|[SGK1](SGK1)|1 |1 |
50
-|[WDR87](WDR87)| |2 |
51
-
52
-# Details
53
-
ganapathiGeneticLandscapeDural2016.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ganapathiGeneticLandscapeDural2016
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MZL Tier 1, 1
26
-This study, MZL Tier 2,
27
-Other MZL studies, MZL Tier 1, 42
28
-Other MZL studies, MZL Tier 2, 74
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MZL tier|
35
-|:-|:-:|
36
-|[KLHL6](KLHL6)|1 |
37
-
38
-# Details
39
-
gomezUltraDeepSequencingReveals2023.md
... ...
@@ -1,45 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @gomezUltraDeepSequencingReveals2023
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|2|5|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 2
26
-This study, PMBL Tier 2, 5
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[ARID5B](ARID5B)|1 |
37
-|[AXDND1](AXDND1)|2 |
38
-|[CDH5](CDH5)|2 |
39
-|[DTX1](DTX1)|1 |
40
-|[HLA-C](HLA-C)|2 |
41
-|[LIMD2](LIMD2)|2 |
42
-|[OR13C2](OR13C2)|2 |
43
-
44
-# Details
45
-
grandeGenomewideDiscoverySomatic2019.md
... ...
@@ -1,51 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @grandeGenomewideDiscoverySomatic2019
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|9|4|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1, 9
26
-This study, BL Tier 2, 4
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[BACH2](BACH2)|2 |
37
-|[BCL7A](BCL7A)|1 |
38
-|[CDKN2A](CDKN2A)|2 |
39
-|[CHD8](CHD8)|1 |
40
-|[GNAI2](GNAI2)|1 |
41
-|[HIST1H1E](HIST1H1E)|2 |
42
-|[KMT2D](KMT2D)|1 |
43
-|[MIR142](MIR142)|2 |
44
-|[RFX7](RFX7)|1 |
45
-|[SIN3A](SIN3A)|1 |
46
-|[TCL1A](TCL1A)|1 |
47
-|[TFAP4](TFAP4)|1 |
48
-|[USP7](USP7)|1 |
49
-
50
-# Details
51
-
gunawardanaRecurrentSomaticMutations2014c.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @gunawardanaRecurrentSomaticMutations2014c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[PTPN1](PTPN1)|1 |
37
-
38
-# Details
39
-
hubschmannMutationalMechanismsShaping2021b.md
... ...
@@ -1,77 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @hubschmannMutationalMechanismsShaping2021b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|2|15|
12
-|DLBCL|3|23|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, DLBCL Tier 1, 3
27
-This study, DLBCL Tier 2, 23
28
-Other DLBCL studies, DLBCL Tier 1, 128
29
-Other DLBCL studies, DLBCL Tier 2, 198
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|FL tier|DLBCL tier|
36
-|:-|:-:|:-:|
37
-|[ACTG1](ACTG1)|2 |1 |
38
-|[ADAMTS1](ADAMTS1)| |2 |
39
-|[ANKRD12](ANKRD12)| |2 |
40
-|[ATP6V1A](ATP6V1A)|2 | |
41
-|[CADPS2](CADPS2)| |2 |
42
-|[CCDC42BPB](CCDC42BPB)|2 | |
43
-|[CNOT2](CNOT2)| |2 |
44
-|[CPNE8](CPNE8)|2 | |
45
-|[DHX15](DHX15)|2 | |
46
-|[DHX16](DHX16)| |2 |
47
-|[DNM2](DNM2)| |2 |
48
-|[EEF1A1](EEF1A1)|1 |1 |
49
-|[FBXO11](FBXO11)| |1 |
50
-|[FZR1](FZR1)|2 | |
51
-|[GAK](GAK)| |2 |
52
-|[HLA-DQA1](HLA-DQA1)| |2 |
53
-|[IKBKE](IKBKE)| |2 |
54
-|[IRF1](IRF1)| |2 |
55
-|[JUP](JUP)|2 | |
56
-|[LAPTM5](LAPTM5)|2 |2 |
57
-|[LRP12](LRP12)| |2 |
58
-|[MGEA5](MGEA5)|2 | |
59
-|[MYCBP2](MYCBP2)|2 | |
60
-|[N2RF2](N2RF2)| |2 |
61
-|[PDS5B](PDS5B)|2 |2 |
62
-|[PNPO](PNPO)| |2 |
63
-|[PPP4C](PPP4C)|2 | |
64
-|[PRKDC](PRKDC)|2 |2 |
65
-|[RAC2](RAC2)| |2 |
66
-|[RBM6](RBM6)|2 | |
67
-|[SIAH2](SIAH2)| |2 |
68
-|[SLC34A2](SLC34A2)| |2 |
69
-|[TPP1](TPP1)|2 | |
70
-|[TRAF6](TRAF6)| |2 |
71
-|[UNC5B](UNC5B)| |2 |
72
-|[VMA21](VMA21)|1 | |
73
-|[WNK1](WNK1)| |2 |
74
-|[ZNF217](ZNF217)| |2 |
75
-
76
-# Details
77
-
images/icons/Tier2_DLBCL.png
... ...
Binary files a/images/icons/Tier2_DLBCL.png and /dev/null differ
jalladesExomeSequencingIdentifies2017.md
... ...
@@ -1,66 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @jalladesExomeSequencingIdentifies2017
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|2|26|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MZL Tier 1, 2
26
-This study, MZL Tier 2, 26
27
-Other MZL studies, MZL Tier 1, 42
28
-Other MZL studies, MZL Tier 2, 74
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MZL tier|
35
-|:-|:-:|
36
-|[ARHGAP20](ARHGAP20)|2 |
37
-|[ARHGEF15](ARHGEF15)|2 |
38
-|[ARHGEF17](ARHGEF17)|2 |
39
-|[BCOR](BCOR)|2 |
40
-|[CCND3](CCND3)|1 |
41
-|[DNAH5](DNAH5)|2 |
42
-|[DNAH7](DNAH7)|2 |
43
-|[DNAI1](DNAI1)|2 |
44
-|[DOCK6](DOCK6)|2 |
45
-|[DTX3L](DTX3L)|2 |
46
-|[EZH1](EZH1)|2 |
47
-|[HIST1H1D](HIST1H1D)|2 |
48
-|[HIST1H2AD](HIST1H2AD)|2 |
49
-|[HIST4H4](HIST4H4)|2 |
50
-|[HRAS](HRAS)|2 |
51
-|[KAT6A](KAT6A)|2 |
52
-|[KDM6A](KDM6A)|2 |
53
-|[KIF26A](KIF26A)|2 |
54
-|[KLF2](KLF2)|1 |
55
-|[MGA](MGA)|2 |
56
-|[MYC](MYC)|2 |
57
-|[MYLK](MYLK)|2 |
58
-|[NCOA6](NCOA6)|2 |
59
-|[NRAS](NRAS)|2 |
60
-|[RAF1](RAF1)|2 |
61
-|[ROCK1](ROCK1)|2 |
62
-|[TBK1](TBK1)|2 |
63
-|[WNK1](WNK1)|2 |
64
-
65
-# Details
66
-
jardinRecurrentMutationsExportin2016a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @jardinRecurrentMutationsExportin2016a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[XPO1](XPO1)|1 |
37
-
38
-# Details
39
-
khodabakhshiRecurrentTargetsAberrant2012.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @khodabakhshiRecurrentTargetsAberrant2012
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[CXCR4](CXCR4)|1 |
37
-
38
-# Details
39
-
krysiakRecurrentSomaticMutations2017b.md
... ...
@@ -1,60 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @krysiakRecurrentSomaticMutations2017b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|17|5|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, FL Tier 1, 17
26
-This study, FL Tier 2, 5
27
-Other FL studies, FL Tier 1, 66
28
-Other FL studies, FL Tier 2, 50
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|FL tier|
35
-|:-|:-:|
36
-|[ARID1A](ARID1A)|1 |
37
-|[BCL7A](BCL7A)|1 |
38
-|[BTK](BTK)|1 |
39
-|[CXCR4](CXCR4)|2 |
40
-|[EGR1](EGR1)|2 |
41
-|[HIST1H1B](HIST1H1B)|1 |
42
-|[HIST1H1D](HIST1H1D)|1 |
43
-|[HIST1H1E](HIST1H1E)|1 |
44
-|[HIST1H2AC](HIST1H2AC)|1 |
45
-|[HIST1H2AG](HIST1H2AG)|1 |
46
-|[HIST1H2AM](HIST1H2AM)|1 |
47
-|[HIST1H2BC](HIST1H2BC)|1 |
48
-|[HIST1H2BD](HIST1H2BD)|1 |
49
-|[HIST1H2BG](HIST1H2BG)|1 |
50
-|[HIST1H2BM](HIST1H2BM)|2 |
51
-|[HIST1H3G](HIST1H3G)|1 |
52
-|[HIST1H3I](HIST1H3I)|2 |
53
-|[HVCN1](HVCN1)|1 |
54
-|[POU2AF1](POU2AF1)|1 |
55
-|[POU2F2](POU2F2)|1 |
56
-|[SMARCA4](SMARCA4)|1 |
57
-|[ZNF608](ZNF608)|2 |
58
-
59
-# Details
60
-
kwanhianMicroRNA142Mutated202012b.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @kwanhianMicroRNA142Mutated202012b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL||1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1,
26
-This study, DLBCL Tier 2, 1
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[MIR142](MIR142)|2 |
37
-
38
-# Details
39
-
lakeMutationsNFKBIAEncoding2009.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @lakeMutationsNFKBIAEncoding2009
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[NFKBIA](NFKBIA)|1 |
37
-
38
-# Details
39
-
lenzOncogenicCARD11Mutations2008.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @lenzOncogenicCARD11Mutations2008
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[CARD11](CARD11)|1 |
37
-
38
-# Details
39
-
lohrDiscoveryPrioritizationSomatic2012a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @lohrDiscoveryPrioritizationSomatic2012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 3
26
-This study, DLBCL Tier 2, 1
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[ACTB](ACTB)|1 |
37
-|[KRAS](KRAS)|1 |
38
-|[P2RY8](P2RY8)|1 |
39
-|[PCLO](PCLO)|2 |
40
-
41
-# Details
42
-
louissaintPediatrictypeNodalFollicular2016a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @louissaintPediatrictypeNodalFollicular2016a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, FL Tier 1, 1
26
-This study, FL Tier 2,
27
-Other FL studies, FL Tier 1, 66
28
-Other FL studies, FL Tier 2, 50
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|FL tier|
35
-|:-|:-:|
36
-|[MAP2K1](MAP2K1)|1 |
37
-
38
-# Details
39
-
loveGeneticLandscapeMutations2012.md
... ...
@@ -1,97 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @loveGeneticLandscapeMutations2012
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|3|56|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1, 3
26
-This study, BL Tier 2, 56
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[ACAD9](ACAD9)|2 |
37
-|[ACE](ACE)|2 |
38
-|[ARID1A](ARID1A)|1 |
39
-|[ATP2C2](ATP2C2)|2 |
40
-|[BCL6](BCL6)|2 |
41
-|[BRAF](BRAF)|2 |
42
-|[BRD4](BRD4)|2 |
43
-|[BTG2](BTG2)|2 |
44
-|[C6orf27](C6orf27)|2 |
45
-|[CAD](CAD)|2 |
46
-|[CARD4](CARD4)|2 |
47
-|[CCT6B](CCT6B)|2 |
48
-|[CDC73](CDC73)|2 |
49
-|[CDH17](CDH17)|2 |
50
-|[COL4A2](COL4A2)|2 |
51
-|[CREBBP](CREBBP)|2 |
52
-|[CYB5D1](CYB5D1)|2 |
53
-|[CYP4F22](CYP4F22)|2 |
54
-|[DLGAP1](DLGAP1)|2 |
55
-|[EIF2C4](EIF2C4)|2 |
56
-|[EML2](EML2)|2 |
57
-|[ENTPD3](ENTPD3)|2 |
58
-|[EPHB2](EPHB2)|2 |
59
-|[EZH2](EZH2)|2 |
60
-|[FAM129B](FAM129B)|2 |
61
-|[FGFR3](FGFR3)|2 |
62
-|[FTCD](FTCD)|2 |
63
-|[GGTLA4](GGTLA4)|2 |
64
-|[GNA13](GNA13)|1 |
65
-|[GRIK5](GRIK5)|2 |
66
-|[ICK](ICK)|2 |
67
-|[ITPR3](ITPR3)|2 |
68
-|[KIFC3](KIFC3)|2 |
69
-|[MAP3K6](MAP3K6)|2 |
70
-|[MYH10](MYH10)|2 |
71
-|[NBEAL1](NBEAL1)|2 |
72
-|[NOTCH1](NOTCH1)|2 |
73
-|[NRXN2](NRXN2)|2 |
74
-|[P2RY2](P2RY2)|2 |
75
-|[PC](PC)|2 |
76
-|[POLRMT](POLRMT)|2 |
77
-|[POR](POR)|2 |
78
-|[PRSS22](PRSS22)|2 |
79
-|[PTEN](PTEN)|1 |
80
-|[PTPRN](PTPRN)|2 |
81
-|[RANBP6](RANBP6)|2 |
82
-|[RBP3](RBP3)|2 |
83
-|[RET](RET)|2 |
84
-|[SALL3](SALL3)|2 |
85
-|[SAPS2](SAPS2)|2 |
86
-|[SBF1](SBF1)|2 |
87
-|[SF3B1](SF3B1)|2 |
88
-|[SHANK1](SHANK1)|2 |
89
-|[SLC29A2](SLC29A2)|2 |
90
-|[SYNGAP1](SYNGAP1)|2 |
91
-|[TBC1D9B](TBC1D9B)|2 |
92
-|[TIGD6](TIGD6)|2 |
93
-|[TPST2](TPST2)|2 |
94
-|[ZNF229](ZNF229)|2 |
95
-
96
-# Details
97
-
mansouriFrequentNFKBIEDeletions2016.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @mansouriFrequentNFKBIEDeletions2016
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[NFKBIE](NFKBIE)|1 |
37
-
38
-# Details
39
-
mareschalWholeExomeSequencing2016.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @mareschalWholeExomeSequencing2016
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 2
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[TBL1XR1](TBL1XR1)|1 |
37
-|[XPO1](XPO1)|1 |
38
-
39
-# Details
40
-
morinFrequentMutationHistonemodifying2011.md
... ...
@@ -1,67 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @morinFrequentMutationHistonemodifying2011
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|19|4|
12
-|DLBCL|27|1|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, DLBCL Tier 1, 27
27
-This study, DLBCL Tier 2, 1
28
-Other DLBCL studies, DLBCL Tier 1, 128
29
-Other DLBCL studies, DLBCL Tier 2, 198
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|FL tier|DLBCL tier|
36
-|:-|:-:|:-:|
37
-|[B2M](B2M)|1 |1 |
38
-|[BCL10](BCL10)|2 |1 |
39
-|[BCL2](BCL2)|1 |1 |
40
-|[BCL6](BCL6)|1 |1 |
41
-|[BTG1](BTG1)|1 |1 |
42
-|[BTG2](BTG2)|1 |1 |
43
-|[CARD11](CARD11)|1 |1 |
44
-|[CCND3](CCND3)|1 |1 |
45
-|[CD274](CD274)| |2 |
46
-|[CD58](CD58)| |1 |
47
-|[CD70](CD70)|2 |1 |
48
-|[CD79B](CD79B)|2 |1 |
49
-|[CIITA](CIITA)| |1 |
50
-|[ETS1](ETS1)| |1 |
51
-|[FOXO1](FOXO1)|1 |1 |
52
-|[GNA13](GNA13)|1 |1 |
53
-|[HIST1H1C](HIST1H1C)|1 |1 |
54
-|[IRF4](IRF4)|1 |1 |
55
-|[IRF8](IRF8)|1 |1 |
56
-|[KLHL6](KLHL6)|1 |1 |
57
-|[KMT2D](KMT2D)|1 |1 |
58
-|[MEF2B](MEF2B)|1 |1 |
59
-|[S1PR2](S1PR2)|1 |1 |
60
-|[SGK1](SGK1)|1 |1 |
61
-|[SOCS1](SOCS1)|1 |1 |
62
-|[TMEM30A](TMEM30A)|2 |1 |
63
-|[TP53](TP53)|1 |1 |
64
-|[ZFP36L1](ZFP36L1)| |1 |
65
-
66
-# Details
67
-
morinGeneticLandscapesRelapsed2016.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @morinGeneticLandscapesRelapsed2016
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 2
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[NFKBIE](NFKBIE)|1 |
37
-|[NFKBIZ](NFKBIZ)|1 |
38
-
39
-# Details
40
-
morinMutationalStructuralAnalysis2013.md
... ...
@@ -1,78 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @morinMutationalStructuralAnalysis2013
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|11|29|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 11
26
-This study, DLBCL Tier 2, 29
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[ABI3BP](ABI3BP)|2 |
37
-|[CD83](CD83)|1 |
38
-|[CDH9](CDH9)|2 |
39
-|[CDKN2A](CDKN2A)|1 |
40
-|[CNTNAP5](CNTNAP5)|2 |
41
-|[DNAH5](DNAH5)|2 |
42
-|[DSG4](DSG4)|2 |
43
-|[DUSP2](DUSP2)|1 |
44
-|[FAM38B](FAM38B)|2 |
45
-|[FAT4](FAT4)|2 |
46
-|[FNDC1](FNDC1)|2 |
47
-|[GNAI2](GNAI2)|1 |
48
-|[HDAC7](HDAC7)|2 |
49
-|[HIST1H1D](HIST1H1D)|1 |
50
-|[HIST1H1E](HIST1H1E)|1 |
51
-|[HIST1H2AC](HIST1H2AC)|1 |
52
-|[HIST1H2AG](HIST1H2AG)|2 |
53
-|[IER2](IER2)|2 |
54
-|[IFNGR1](IFNGR1)|2 |
55
-|[IKZF3](IKZF3)|1 |
56
-|[LRRN3](LRRN3)|2 |
57
-|[MPDZ](MPDZ)|2 |
58
-|[MPEG1](MPEG1)|1 |
59
-|[NLRP5](NLRP5)|2 |
60
-|[ODZ3](ODZ3)|2 |
61
-|[P2RX5](P2RX5)|2 |
62
-|[PASK](PASK)|2 |
63
-|[PCDHB11](PCDHB11)|2 |
64
-|[PDS5B](PDS5B)|2 |
65
-|[PKD1](PKD1)|2 |
66
-|[POGZ](POGZ)|2 |
67
-|[PRKCB](PRKCB)|2 |
68
-|[PTPN23](PTPN23)|2 |
69
-|[RB1](RB1)|1 |
70
-|[SAMD9L](SAMD9L)|2 |
71
-|[SARM1](SARM1)|2 |
72
-|[SRRM2](SRRM2)|2 |
73
-|[SYPL1](SYPL1)|2 |
74
-|[TAF1](TAF1)|1 |
75
-|[WDFY3](WDFY3)|2 |
76
-
77
-# Details
78
-
morinSomaticMutationsAltering2010a.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @morinSomaticMutationsAltering2010a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-|FL|1||
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, DLBCL Tier 1, 1
27
-This study, DLBCL Tier 2,
28
-Other DLBCL studies, DLBCL Tier 1, 128
29
-Other DLBCL studies, DLBCL Tier 2, 198
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|DLBCL tier|FL tier|
36
-|:-|:-:|:-:|
37
-|[EZH2](EZH2)|1 |1 |
38
-
39
-# Details
40
-
mottokGenomicAlterationsCIITA2015b.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @mottokGenomicAlterationsCIITA2015b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[CIITA](CIITA)|1 |
37
-
38
-# Details
39
-
mottokIntegrativeGenomicAnalysis2019b.md
... ...
@@ -1,59 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @mottokIntegrativeGenomicAnalysis2019b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|6|15|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 6
26
-This study, PMBL Tier 2, 15
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[CISH](CISH)|1 |
37
-|[CXCR5](CXCR5)|2 |
38
-|[DDX3X](DDX3X)|1 |
39
-|[EPHA7](EPHA7)|2 |
40
-|[EZH2](EZH2)|1 |
41
-|[GCSAM](GCSAM)|2 |
42
-|[HIST1H2BC](HIST1H2BC)|2 |
43
-|[HIST1H4E](HIST1H4E)|2 |
44
-|[HIST1H4J](HIST1H4J)|2 |
45
-|[IL13RA1](IL13RA1)|2 |
46
-|[IL1RAPL2](IL1RAPL2)|2 |
47
-|[IRF2BP2](IRF2BP2)|2 |
48
-|[IRF4](IRF4)|2 |
49
-|[IRF8](IRF8)|1 |
50
-|[JAK1](JAK1)|1 |
51
-|[JUNB](JUNB)|2 |
52
-|[MAGEC2](MAGEC2)|2 |
53
-|[MS4A1](MS4A1)|1 |
54
-|[NFKB2](NFKB2)|2 |
55
-|[RGS1](RGS1)|2 |
56
-|[VMP1](VMP1)|2 |
57
-
58
-# Details
59
-
muppidiLossSignalingGa132014b.md
... ...
@@ -1,41 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @muppidiLossSignalingGa132014b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1, 1
26
-This study, BL Tier 2, 2
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[ARHGEF1](ARHGEF1)|2 |
37
-|[P2RY8](P2RY8)|1 |
38
-|[S1PR2](S1PR2)|2 |
39
-
40
-# Details
41
-
nadeuGenomicEpigenomicInsights2020b.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @nadeuGenomicEpigenomicInsights2020b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|3|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MCL Tier 1, 3
26
-This study, MCL Tier 2, 2
27
-Other MCL studies, MCL Tier 1, 23
28
-Other MCL studies, MCL Tier 2, 46
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MCL tier|
35
-|:-|:-:|
36
-|[BCOR](BCOR)|2 |
37
-|[SMARCA4](SMARCA4)|1 |
38
-|[SMARCB1](SMARCB1)|2 |
39
-|[SYNE1](SYNE1)|1 |
40
-|[TERT](TERT)|1 |
41
-
42
-# Details
43
-
ngoOncogenicallyActiveMYD882011a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ngoOncogenicallyActiveMYD882011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[MYD88](MYD88)|1 |
37
-
38
-# Details
39
-
ohgamiSTAT3MutationsAre2014.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ohgamiSTAT3MutationsAre2014
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[STAT3](STAT3)|1 |
37
-
38
-# Details
39
-
okosunRecurrentMTORC1activatingRRAGC2016a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @okosunRecurrentMTORC1activatingRRAGC2016a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-|FL|3||
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, FL Tier 1, 3
27
-This study, FL Tier 2,
28
-Other FL studies, FL Tier 1, 66
29
-Other FL studies, FL Tier 2, 50
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|DLBCL tier|FL tier|
36
-|:-|:-:|:-:|
37
-|[ATP6AP1](ATP6AP1)| |1 |
38
-|[ATP6V1B2](ATP6V1B2)| |1 |
39
-|[RRAGC](RRAGC)|1 |1 |
40
-
41
-# Details
42
-
oricchioGeneticEpigeneticInactivation2017b.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @oricchioGeneticEpigeneticInactivation2017b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL||1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, FL Tier 1,
26
-This study, FL Tier 2, 1
27
-Other FL studies, FL Tier 1, 66
28
-Other FL studies, FL Tier 2, 50
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|FL tier|
35
-|:-|:-:|
36
-|[SESN1](SESN1)|2 |
37
-
38
-# Details
39
-
ottoGeneticLesionsTRAF32012a.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ottoGeneticLesionsTRAF32012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|2||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 2
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[MAP3K14](MAP3K14)|1 |
37
-|[TRAF3](TRAF3)|1 |
38
-
39
-# Details
40
-
paneaWholeGenomeLandscape2019.md
... ...
@@ -1,90 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @paneaWholeGenomeLandscape2019
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|4|46|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: left
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 4
26
-New Tier 1, BL Tier 1, 4
27
-This study, New Tier 2, 46
28
-New Tier 2, BL Tier 2, 46
29
-Other BL studies, BL Tier 1, 29
30
-Other BL studies, BL Tier 2, 157
31
-```
32
-
33
-
34
-## Novel genes reported in this study
35
-
36
-|New gene|BL tier|
37
-|:-|:-:|
38
-|[ALPK2](ALPK2)|2 |
39
-|[BMP7](BMP7)|1 |
40
-|[CARD11](CARD11)|2 |
41
-|[CD79B](CD79B)|2 |
42
-|[CD83](CD83)|2 |
43
-|[CTCF](CTCF)|2 |
44
-|[CXCR4](CXCR4)|2 |
45
-|[DNMT1](DNMT1)|2 |
46
-|[DTX1](DTX1)|2 |
47
-|[EIF4A1](EIF4A1)|1 |
48
-|[EP300](EP300)|2 |
49
-|[EPPK1](EPPK1)|1 |
50
-|[ETS1](ETS1)|2 |
51
-|[FZD3](FZD3)|2 |
52
-|[GRB2](GRB2)|2 |
53
-|[HIST1H1C](HIST1H1C)|2 |
54
-|[HIST1H2AG](HIST1H2AG)|2 |
55
-|[HIST1H2AM](HIST1H2AM)|2 |
56
-|[HIST1H2BK](HIST1H2BK)|2 |
57
-|[HIST1H3D](HIST1H3D)|2 |
58
-|[HIST1H3H](HIST1H3H)|2 |
59
-|[HIST1H3I](HIST1H3I)|2 |
60
-|[HIST1H3J](HIST1H3J)|2 |
61
-|[HIST1H4J](HIST1H4J)|2 |
62
-|[HNRNPU](HNRNPU)|1 |
63
-|[IGLL5](IGLL5)|2 |
64
-|[IKZF3](IKZF3)|2 |
65
-|[IRF8](IRF8)|2 |
66
-|[KCNK10](KCNK10)|2 |
67
-|[KLHL6](KLHL6)|2 |
68
-|[LTB](LTB)|2 |
69
-|[MCL1](MCL1)|2 |
70
-|[MME](MME)|2 |
71
-|[MTOR](MTOR)|2 |
72
-|[NOTCH2](NOTCH2)|2 |
73
-|[PABPC4L](PABPC4L)|2 |
74
-|[PCDHA11](PCDHA11)|2 |
75
-|[PDZRN3](PDZRN3)|2 |
76
-|[PIK3R1](PIK3R1)|2 |
77
-|[PLCG2](PLCG2)|2 |
78
-|[PXDNL](PXDNL)|2 |
79
-|[RAC2](RAC2)|2 |
80
-|[RNF144B](RNF144B)|2 |
81
-|[SNTB2](SNTB2)|2 |
82
-|[SP3](SP3)|2 |
83
-|[SYNCRIP](SYNCRIP)|2 |
84
-|[TET2](TET2)|2 |
85
-|[WDR7](WDR7)|2 |
86
-|[WNK2](WNK2)|2 |
87
-|[ZFP36L1](ZFP36L1)|2 |
88
-
89
-# Details
90
-
papers/abateDistinctViralMutational2015a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @abateDistinctViralMutational2015a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL||1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1,
26
+This study, BL Tier 2, 1
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[CCNF](CCNF)|2 |
37
+
38
+# Details
39
+
papers/albuquerqueEnhancingKnowledgeDiscovery2017a.md
... ...
@@ -0,0 +1,44 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @albuquerqueEnhancingKnowledgeDiscovery2017a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|3||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 3
26
+New Tier 1, DLBCL Tier 1, 3
27
+This study, DLBCL Tier 2,
28
+This study, New Tier 2,
29
+New Tier 2, DLBCL Tier 2,
30
+Other DLBCL studies, DLBCL Tier 1, 128
31
+Other DLBCL studies, DLBCL Tier 2, 198
32
+```
33
+
34
+
35
+## Novel genes reported in this study
36
+
37
+|New gene|DLBCL tier|
38
+|:-|:-:|
39
+|[BTK](BTK)|1 |
40
+|[TET2](TET2)|1 |
41
+|[TMSB4X](TMSB4X)|1 |
42
+
43
+# Details
44
+
papers/arthurGenomewideDiscoverySomatic2018.md
... ...
@@ -0,0 +1,58 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @arthurGenomewideDiscoverySomatic2018
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|8|12|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 8
26
+This study, DLBCL Tier 2, 12
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[AICDA](AICDA)|2 |
37
+|[BCL7A](BCL7A)|1 |
38
+|[BIRC3](BIRC3)|2 |
39
+|[CD44](CD44)|2 |
40
+|[CD74](CD74)|2 |
41
+|[ETV6](ETV6)|1 |
42
+|[GRHPR](GRHPR)|1 |
43
+|[LCOR](LCOR)|1 |
44
+|[LPP](LPP)|2 |
45
+|[MALAT1](MALAT1)|2 |
46
+|[MEF2C](MEF2C)|1 |
47
+|[NEAT1](NEAT1)|2 |
48
+|[OSBPL10](OSBPL10)|1 |
49
+|[PIM2](PIM2)|1 |
50
+|[RFTN1](RFTN1)|2 |
51
+|[SERPINA9](SERPINA9)|2 |
52
+|[ST6GAL1](ST6GAL1)|2 |
53
+|[TBC1D4](TBC1D4)|2 |
54
+|[ZC3H12A](ZC3H12A)|1 |
55
+|[ZCCHC7](ZCCHC7)|2 |
56
+
57
+# Details
58
+
papers/barariaCathepsinAlterationsInduce2020c.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @barariaCathepsinAlterationsInduce2020c
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, FL Tier 1, 1
26
+This study, FL Tier 2,
27
+Other FL studies, FL Tier 1, 66
28
+Other FL studies, FL Tier 2, 50
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|FL tier|
35
+|:-|:-:|
36
+|[CTSS](CTSS)|1 |
37
+
38
+# Details
39
+
papers/beaLandscapeSomaticMutations2013.md
... ...
@@ -0,0 +1,65 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @beaLandscapeSomaticMutations2013
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MCL|11|16|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MCL Tier 1, 11
26
+This study, MCL Tier 2, 16
27
+Other MCL studies, MCL Tier 1, 23
28
+Other MCL studies, MCL Tier 2, 46
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MCL tier|
35
+|:-|:-:|
36
+|[ABCA3](ABCA3)|2 |
37
+|[ABCC9](ABCC9)|2 |
38
+|[ATM](ATM)|1 |
39
+|[BIRC3](BIRC3)|1 |
40
+|[CCND1](CCND1)|1 |
41
+|[CHMP4C](CHMP4C)|2 |
42
+|[CRYBG3](CRYBG3)|2 |
43
+|[DCP1B](DCP1B)|2 |
44
+|[DLGAP2](DLGAP2)|2 |
45
+|[DNAJC6](DNAJC6)|2 |
46
+|[KCNC2](KCNC2)|2 |
47
+|[KIAA1671](KIAA1671)|2 |
48
+|[KMT2D](KMT2D)|1 |
49
+|[LUZP4](LUZP4)|2 |
50
+|[MEF2B](MEF2B)|1 |
51
+|[NOTCH1](NOTCH1)|1 |
52
+|[NOTCH2](NOTCH2)|1 |
53
+|[NSD2](NSD2)|1 |
54
+|[PCSK2](PCSK2)|2 |
55
+|[PDLIM3](PDLIM3)|2 |
56
+|[RGS4](RGS4)|2 |
57
+|[SLC17A6](SLC17A6)|2 |
58
+|[SP140](SP140)|1 |
59
+|[TLR2](TLR2)|1 |
60
+|[TNRC6B](TNRC6B)|2 |
61
+|[TP53](TP53)|1 |
62
+|[TRPM6](TRPM6)|2 |
63
+
64
+# Details
65
+
papers/bohleRoleEarlyBcell2013.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @bohleRoleEarlyBcell2013
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[EBF1](EBF1)|1 |
37
+
38
+# Details
39
+
papers/braggioGenomicAnalysisMarginal2012.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @braggioGenomicAnalysisMarginal2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MZL Tier 1, 1
26
+This study, MZL Tier 2,
27
+Other MZL studies, MZL Tier 1, 42
28
+Other MZL studies, MZL Tier 2, 74
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MZL tier|
35
+|:-|:-:|
36
+|[ATM](ATM)|1 |
37
+
38
+# Details
39
+
papers/burkhardtClinicalRelevanceMolecular2022b.md
... ...
@@ -0,0 +1,63 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @burkhardtClinicalRelevanceMolecular2022b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL||25|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1,
26
+This study, BL Tier 2, 25
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[ADAMTS5](ADAMTS5)|2 |
37
+|[ADNP](ADNP)|2 |
38
+|[AGO4](AGO4)|2 |
39
+|[BCL2](BCL2)|2 |
40
+|[BTG1](BTG1)|2 |
41
+|[CD79A](CD79A)|2 |
42
+|[CHD4](CHD4)|2 |
43
+|[CPXM2](CPXM2)|2 |
44
+|[E2F2](E2F2)|2 |
45
+|[EDNRB](EDNRB)|2 |
46
+|[ERAP1](ERAP1)|2 |
47
+|[HLA-DQB1](HLA-DQB1)|2 |
48
+|[KLHL26](KLHL26)|2 |
49
+|[NOA1](NOA1)|2 |
50
+|[PIM1](PIM1)|2 |
51
+|[PPP6R2](PPP6R2)|2 |
52
+|[PREX1](PREX1)|2 |
53
+|[REV3L](REV3L)|2 |
54
+|[RPL10](RPL10)|2 |
55
+|[SAL3](SAL3)|2 |
56
+|[TTN](TTN)|2 |
57
+|[VWA7](VWA7)|2 |
58
+|[ZAN](ZAN)|2 |
59
+|[ZBTB7A](ZBTB7A)|2 |
60
+|[ZNF85](ZNF85)|2 |
61
+
62
+# Details
63
+
papers/chapuyMolecularSubtypesDiffuse2018b.md
... ...
@@ -0,0 +1,57 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @chapuyMolecularSubtypesDiffuse2018b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|2|17|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 2
26
+This study, DLBCL Tier 2, 17
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[CCL4](CCL4)|2 |
37
+|[COQ7](COQ7)|2 |
38
+|[CRIP1](CRIP1)|2 |
39
+|[DOCK1](DOCK1)|2 |
40
+|[FUT5](FUT5)|2 |
41
+|[GABRA2](GABRA2)|2 |
42
+|[HIST1H1B](HIST1H1B)|1 |
43
+|[IL6](IL6)|2 |
44
+|[LTB](LTB)|1 |
45
+|[LYN](LYN)|2 |
46
+|[NANOG](NANOG)|2 |
47
+|[NAV1](NAV1)|2 |
48
+|[NLRP8](NLRP8)|2 |
49
+|[PDE4DIP](PDE4DIP)|2 |
50
+|[PRPS1](PRPS1)|2 |
51
+|[RAD9A](RAD9A)|2 |
52
+|[SMEK1](SMEK1)|2 |
53
+|[TLR2](TLR2)|2 |
54
+|[ZNF423](ZNF423)|2 |
55
+
56
+# Details
57
+
papers/cheungAcquiredTNFRSF14Mutations2010a.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @cheungAcquiredTNFRSF14Mutations2010a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+|FL|1||
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, DLBCL Tier 1, 1
27
+This study, DLBCL Tier 2,
28
+Other DLBCL studies, DLBCL Tier 1, 128
29
+Other DLBCL studies, DLBCL Tier 2, 198
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|DLBCL tier|FL tier|
36
+|:-|:-:|:-:|
37
+|[TNFRSF14](TNFRSF14)|1 |1 |
38
+
39
+# Details
40
+
papers/compagnoMutationsMultipleGenes2009a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @compagnoMutationsMultipleGenes2009a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[TNFAIP3](TNFAIP3)|1 |
37
+
38
+# Details
39
+
papers/deschGenotypingCirculatingTumor2020.md
... ...
@@ -0,0 +1,48 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @deschGenotypingCirculatingTumor2020
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1|9|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2, 9
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[ACTG1](ACTG1)|2 |
37
+|[CCND3](CCND3)|2 |
38
+|[CDH2](CDH2)|2 |
39
+|[EZR](EZR)|2 |
40
+|[HLA-A](HLA-A)|2 |
41
+|[IGLL5](IGLL5)|2 |
42
+|[KLF2](KLF2)|2 |
43
+|[KMT2D](KMT2D)|2 |
44
+|[LTB](LTB)|1 |
45
+|[MYB](MYB)|2 |
46
+
47
+# Details
48
+
papers/dunsCharacterizationDLBCLPMBL2021b.md
... ...
@@ -0,0 +1,53 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @dunsCharacterizationDLBCLPMBL2021b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|8|3|
12
+|PMBL|6|8|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, PMBL Tier 1, 6
27
+This study, PMBL Tier 2, 8
28
+Other PMBL studies, PMBL Tier 1, 76
29
+Other PMBL studies, PMBL Tier 2, 82
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|DLBCL tier|PMBL tier|
36
+|:-|:-:|:-:|
37
+|[BIRC3](BIRC3)|2 |2 |
38
+|[CD83](CD83)|1 |1 |
39
+|[CREBBP](CREBBP)|1 |1 |
40
+|[DUSP2](DUSP2)|1 |1 |
41
+|[FOXO1](FOXO1)|1 |2 |
42
+|[HRNR](HRNR)| |2 |
43
+|[IL4R](IL4R)|1 |1 |
44
+|[LPHN3](LPHN3)| |2 |
45
+|[MCL1](MCL1)|2 |2 |
46
+|[MYC](MYC)|1 |2 |
47
+|[PIM1](PIM1)|1 |1 |
48
+|[RFTN1](RFTN1)|2 |2 |
49
+|[SGK1](SGK1)|1 |1 |
50
+|[WDR87](WDR87)| |2 |
51
+
52
+# Details
53
+
papers/ganapathiGeneticLandscapeDural2016.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ganapathiGeneticLandscapeDural2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MZL Tier 1, 1
26
+This study, MZL Tier 2,
27
+Other MZL studies, MZL Tier 1, 42
28
+Other MZL studies, MZL Tier 2, 74
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MZL tier|
35
+|:-|:-:|
36
+|[KLHL6](KLHL6)|1 |
37
+
38
+# Details
39
+
papers/gomezUltraDeepSequencingReveals2023.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @gomezUltraDeepSequencingReveals2023
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|2|5|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 2
26
+This study, PMBL Tier 2, 5
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[ARID5B](ARID5B)|1 |
37
+|[AXDND1](AXDND1)|2 |
38
+|[CDH5](CDH5)|2 |
39
+|[DTX1](DTX1)|1 |
40
+|[HLA-C](HLA-C)|2 |
41
+|[LIMD2](LIMD2)|2 |
42
+|[OR13C2](OR13C2)|2 |
43
+
44
+# Details
45
+
papers/grandeGenomewideDiscoverySomatic2019.md
... ...
@@ -0,0 +1,51 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @grandeGenomewideDiscoverySomatic2019
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|9|4|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1, 9
26
+This study, BL Tier 2, 4
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[BACH2](BACH2)|2 |
37
+|[BCL7A](BCL7A)|1 |
38
+|[CDKN2A](CDKN2A)|2 |
39
+|[CHD8](CHD8)|1 |
40
+|[GNAI2](GNAI2)|1 |
41
+|[HIST1H1E](HIST1H1E)|2 |
42
+|[KMT2D](KMT2D)|1 |
43
+|[MIR142](MIR142)|2 |
44
+|[RFX7](RFX7)|1 |
45
+|[SIN3A](SIN3A)|1 |
46
+|[TCL1A](TCL1A)|1 |
47
+|[TFAP4](TFAP4)|1 |
48
+|[USP7](USP7)|1 |
49
+
50
+# Details
51
+
papers/gunawardanaRecurrentSomaticMutations2014c.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @gunawardanaRecurrentSomaticMutations2014c
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[PTPN1](PTPN1)|1 |
37
+
38
+# Details
39
+
papers/hubschmannMutationalMechanismsShaping2021b.md
... ...
@@ -0,0 +1,77 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @hubschmannMutationalMechanismsShaping2021b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|2|15|
12
+|DLBCL|3|23|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, DLBCL Tier 1, 3
27
+This study, DLBCL Tier 2, 23
28
+Other DLBCL studies, DLBCL Tier 1, 128
29
+Other DLBCL studies, DLBCL Tier 2, 198
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|FL tier|DLBCL tier|
36
+|:-|:-:|:-:|
37
+|[ACTG1](ACTG1)|2 |1 |
38
+|[ADAMTS1](ADAMTS1)| |2 |
39
+|[ANKRD12](ANKRD12)| |2 |
40
+|[ATP6V1A](ATP6V1A)|2 | |
41
+|[CADPS2](CADPS2)| |2 |
42
+|[CCDC42BPB](CCDC42BPB)|2 | |
43
+|[CNOT2](CNOT2)| |2 |
44
+|[CPNE8](CPNE8)|2 | |
45
+|[DHX15](DHX15)|2 | |
46
+|[DHX16](DHX16)| |2 |
47
+|[DNM2](DNM2)| |2 |
48
+|[EEF1A1](EEF1A1)|1 |1 |
49
+|[FBXO11](FBXO11)| |1 |
50
+|[FZR1](FZR1)|2 | |
51
+|[GAK](GAK)| |2 |
52
+|[HLA-DQA1](HLA-DQA1)| |2 |
53
+|[IKBKE](IKBKE)| |2 |
54
+|[IRF1](IRF1)| |2 |
55
+|[JUP](JUP)|2 | |
56
+|[LAPTM5](LAPTM5)|2 |2 |
57
+|[LRP12](LRP12)| |2 |
58
+|[MGEA5](MGEA5)|2 | |
59
+|[MYCBP2](MYCBP2)|2 | |
60
+|[N2RF2](N2RF2)| |2 |
61
+|[PDS5B](PDS5B)|2 |2 |
62
+|[PNPO](PNPO)| |2 |
63
+|[PPP4C](PPP4C)|2 | |
64
+|[PRKDC](PRKDC)|2 |2 |
65
+|[RAC2](RAC2)| |2 |
66
+|[RBM6](RBM6)|2 | |
67
+|[SIAH2](SIAH2)| |2 |
68
+|[SLC34A2](SLC34A2)| |2 |
69
+|[TPP1](TPP1)|2 | |
70
+|[TRAF6](TRAF6)| |2 |
71
+|[UNC5B](UNC5B)| |2 |
72
+|[VMA21](VMA21)|1 | |
73
+|[WNK1](WNK1)| |2 |
74
+|[ZNF217](ZNF217)| |2 |
75
+
76
+# Details
77
+
papers/jalladesExomeSequencingIdentifies2017.md
... ...
@@ -0,0 +1,66 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @jalladesExomeSequencingIdentifies2017
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL|2|26|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MZL Tier 1, 2
26
+This study, MZL Tier 2, 26
27
+Other MZL studies, MZL Tier 1, 42
28
+Other MZL studies, MZL Tier 2, 74
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MZL tier|
35
+|:-|:-:|
36
+|[ARHGAP20](ARHGAP20)|2 |
37
+|[ARHGEF15](ARHGEF15)|2 |
38
+|[ARHGEF17](ARHGEF17)|2 |
39
+|[BCOR](BCOR)|2 |
40
+|[CCND3](CCND3)|1 |
41
+|[DNAH5](DNAH5)|2 |
42
+|[DNAH7](DNAH7)|2 |
43
+|[DNAI1](DNAI1)|2 |
44
+|[DOCK6](DOCK6)|2 |
45
+|[DTX3L](DTX3L)|2 |
46
+|[EZH1](EZH1)|2 |
47
+|[HIST1H1D](HIST1H1D)|2 |
48
+|[HIST1H2AD](HIST1H2AD)|2 |
49
+|[HIST4H4](HIST4H4)|2 |
50
+|[HRAS](HRAS)|2 |
51
+|[KAT6A](KAT6A)|2 |
52
+|[KDM6A](KDM6A)|2 |
53
+|[KIF26A](KIF26A)|2 |
54
+|[KLF2](KLF2)|1 |
55
+|[MGA](MGA)|2 |
56
+|[MYC](MYC)|2 |
57
+|[MYLK](MYLK)|2 |
58
+|[NCOA6](NCOA6)|2 |
59
+|[NRAS](NRAS)|2 |
60
+|[RAF1](RAF1)|2 |
61
+|[ROCK1](ROCK1)|2 |
62
+|[TBK1](TBK1)|2 |
63
+|[WNK1](WNK1)|2 |
64
+
65
+# Details
66
+
papers/jardinRecurrentMutationsExportin2016a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @jardinRecurrentMutationsExportin2016a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[XPO1](XPO1)|1 |
37
+
38
+# Details
39
+
papers/johnstonCmycHypermutationBurkitt1992.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @johnstonCmycHypermutationBurkitt1992
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1, 1
26
+This study, BL Tier 2,
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[MYC](MYC)|1 |
37
+
38
+# Details
39
+
papers/khodabakhshiRecurrentTargetsAberrant2012.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @khodabakhshiRecurrentTargetsAberrant2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[CXCR4](CXCR4)|1 |
37
+
38
+# Details
39
+
papers/krysiakRecurrentSomaticMutations2017b.md
... ...
@@ -0,0 +1,60 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @krysiakRecurrentSomaticMutations2017b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|17|5|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, FL Tier 1, 17
26
+This study, FL Tier 2, 5
27
+Other FL studies, FL Tier 1, 66
28
+Other FL studies, FL Tier 2, 50
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|FL tier|
35
+|:-|:-:|
36
+|[ARID1A](ARID1A)|1 |
37
+|[BCL7A](BCL7A)|1 |
38
+|[BTK](BTK)|1 |
39
+|[CXCR4](CXCR4)|2 |
40
+|[EGR1](EGR1)|2 |
41
+|[HIST1H1B](HIST1H1B)|1 |
42
+|[HIST1H1D](HIST1H1D)|1 |
43
+|[HIST1H1E](HIST1H1E)|1 |
44
+|[HIST1H2AC](HIST1H2AC)|1 |
45
+|[HIST1H2AG](HIST1H2AG)|1 |
46
+|[HIST1H2AM](HIST1H2AM)|1 |
47
+|[HIST1H2BC](HIST1H2BC)|1 |
48
+|[HIST1H2BD](HIST1H2BD)|1 |
49
+|[HIST1H2BG](HIST1H2BG)|1 |
50
+|[HIST1H2BM](HIST1H2BM)|2 |
51
+|[HIST1H3G](HIST1H3G)|1 |
52
+|[HIST1H3I](HIST1H3I)|2 |
53
+|[HVCN1](HVCN1)|1 |
54
+|[POU2AF1](POU2AF1)|1 |
55
+|[POU2F2](POU2F2)|1 |
56
+|[SMARCA4](SMARCA4)|1 |
57
+|[ZNF608](ZNF608)|2 |
58
+
59
+# Details
60
+
papers/kwanhianMicroRNA142Mutated202012b.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @kwanhianMicroRNA142Mutated202012b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL||1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1,
26
+This study, DLBCL Tier 2, 1
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[MIR142](MIR142)|2 |
37
+
38
+# Details
39
+
papers/lakeMutationsNFKBIAEncoding2009.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @lakeMutationsNFKBIAEncoding2009
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[NFKBIA](NFKBIA)|1 |
37
+
38
+# Details
39
+
papers/lenzOncogenicCARD11Mutations2008.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @lenzOncogenicCARD11Mutations2008
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[CARD11](CARD11)|1 |
37
+
38
+# Details
39
+
papers/lohrDiscoveryPrioritizationSomatic2012a.md
... ...
@@ -0,0 +1,42 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @lohrDiscoveryPrioritizationSomatic2012a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|3|1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 3
26
+This study, DLBCL Tier 2, 1
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[ACTB](ACTB)|1 |
37
+|[KRAS](KRAS)|1 |
38
+|[P2RY8](P2RY8)|1 |
39
+|[PCLO](PCLO)|2 |
40
+
41
+# Details
42
+
papers/louissaintPediatrictypeNodalFollicular2016a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @louissaintPediatrictypeNodalFollicular2016a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, FL Tier 1, 1
26
+This study, FL Tier 2,
27
+Other FL studies, FL Tier 1, 66
28
+Other FL studies, FL Tier 2, 50
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|FL tier|
35
+|:-|:-:|
36
+|[MAP2K1](MAP2K1)|1 |
37
+
38
+# Details
39
+
papers/loveGeneticLandscapeMutations2012.md
... ...
@@ -0,0 +1,97 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @loveGeneticLandscapeMutations2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|3|56|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1, 3
26
+This study, BL Tier 2, 56
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[ACAD9](ACAD9)|2 |
37
+|[ACE](ACE)|2 |
38
+|[ARID1A](ARID1A)|1 |
39
+|[ATP2C2](ATP2C2)|2 |
40
+|[BCL6](BCL6)|2 |
41
+|[BRAF](BRAF)|2 |
42
+|[BRD4](BRD4)|2 |
43
+|[BTG2](BTG2)|2 |
44
+|[C6orf27](C6orf27)|2 |
45
+|[CAD](CAD)|2 |
46
+|[CARD4](CARD4)|2 |
47
+|[CCT6B](CCT6B)|2 |
48
+|[CDC73](CDC73)|2 |
49
+|[CDH17](CDH17)|2 |
50
+|[COL4A2](COL4A2)|2 |
51
+|[CREBBP](CREBBP)|2 |
52
+|[CYB5D1](CYB5D1)|2 |
53
+|[CYP4F22](CYP4F22)|2 |
54
+|[DLGAP1](DLGAP1)|2 |
55
+|[EIF2C4](EIF2C4)|2 |
56
+|[EML2](EML2)|2 |
57
+|[ENTPD3](ENTPD3)|2 |
58
+|[EPHB2](EPHB2)|2 |
59
+|[EZH2](EZH2)|2 |
60
+|[FAM129B](FAM129B)|2 |
61
+|[FGFR3](FGFR3)|2 |
62
+|[FTCD](FTCD)|2 |
63
+|[GGTLA4](GGTLA4)|2 |
64
+|[GNA13](GNA13)|1 |
65
+|[GRIK5](GRIK5)|2 |
66
+|[ICK](ICK)|2 |
67
+|[ITPR3](ITPR3)|2 |
68
+|[KIFC3](KIFC3)|2 |
69
+|[MAP3K6](MAP3K6)|2 |
70
+|[MYH10](MYH10)|2 |
71
+|[NBEAL1](NBEAL1)|2 |
72
+|[NOTCH1](NOTCH1)|2 |
73
+|[NRXN2](NRXN2)|2 |
74
+|[P2RY2](P2RY2)|2 |
75
+|[PC](PC)|2 |
76
+|[POLRMT](POLRMT)|2 |
77
+|[POR](POR)|2 |
78
+|[PRSS22](PRSS22)|2 |
79
+|[PTEN](PTEN)|1 |
80
+|[PTPRN](PTPRN)|2 |
81
+|[RANBP6](RANBP6)|2 |
82
+|[RBP3](RBP3)|2 |
83
+|[RET](RET)|2 |
84
+|[SALL3](SALL3)|2 |
85
+|[SAPS2](SAPS2)|2 |
86
+|[SBF1](SBF1)|2 |
87
+|[SF3B1](SF3B1)|2 |
88
+|[SHANK1](SHANK1)|2 |
89
+|[SLC29A2](SLC29A2)|2 |
90
+|[SYNGAP1](SYNGAP1)|2 |
91
+|[TBC1D9B](TBC1D9B)|2 |
92
+|[TIGD6](TIGD6)|2 |
93
+|[TPST2](TPST2)|2 |
94
+|[ZNF229](ZNF229)|2 |
95
+
96
+# Details
97
+
papers/mansouriFrequentNFKBIEDeletions2016.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @mansouriFrequentNFKBIEDeletions2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[NFKBIE](NFKBIE)|1 |
37
+
38
+# Details
39
+
papers/mareschalWholeExomeSequencing2016.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @mareschalWholeExomeSequencing2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|2||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 2
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[TBL1XR1](TBL1XR1)|1 |
37
+|[XPO1](XPO1)|1 |
38
+
39
+# Details
40
+
papers/morinFrequentMutationHistonemodifying2011.md
... ...
@@ -0,0 +1,67 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @morinFrequentMutationHistonemodifying2011
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|19|4|
12
+|DLBCL|27|1|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, DLBCL Tier 1, 27
27
+This study, DLBCL Tier 2, 1
28
+Other DLBCL studies, DLBCL Tier 1, 128
29
+Other DLBCL studies, DLBCL Tier 2, 198
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|FL tier|DLBCL tier|
36
+|:-|:-:|:-:|
37
+|[B2M](B2M)|1 |1 |
38
+|[BCL10](BCL10)|2 |1 |
39
+|[BCL2](BCL2)|1 |1 |
40
+|[BCL6](BCL6)|1 |1 |
41
+|[BTG1](BTG1)|1 |1 |
42
+|[BTG2](BTG2)|1 |1 |
43
+|[CARD11](CARD11)|1 |1 |
44
+|[CCND3](CCND3)|1 |1 |
45
+|[CD274](CD274)| |2 |
46
+|[CD58](CD58)| |1 |
47
+|[CD70](CD70)|2 |1 |
48
+|[CD79B](CD79B)|2 |1 |
49
+|[CIITA](CIITA)| |1 |
50
+|[ETS1](ETS1)| |1 |
51
+|[FOXO1](FOXO1)|1 |1 |
52
+|[GNA13](GNA13)|1 |1 |
53
+|[HIST1H1C](HIST1H1C)|1 |1 |
54
+|[IRF4](IRF4)|1 |1 |
55
+|[IRF8](IRF8)|1 |1 |
56
+|[KLHL6](KLHL6)|1 |1 |
57
+|[KMT2D](KMT2D)|1 |1 |
58
+|[MEF2B](MEF2B)|1 |1 |
59
+|[S1PR2](S1PR2)|1 |1 |
60
+|[SGK1](SGK1)|1 |1 |
61
+|[SOCS1](SOCS1)|1 |1 |
62
+|[TMEM30A](TMEM30A)|2 |1 |
63
+|[TP53](TP53)|1 |1 |
64
+|[ZFP36L1](ZFP36L1)| |1 |
65
+
66
+# Details
67
+
papers/morinGeneticLandscapesRelapsed2016.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @morinGeneticLandscapesRelapsed2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|2||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 2
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[NFKBIE](NFKBIE)|1 |
37
+|[NFKBIZ](NFKBIZ)|1 |
38
+
39
+# Details
40
+
papers/morinMutationalStructuralAnalysis2013.md
... ...
@@ -0,0 +1,78 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @morinMutationalStructuralAnalysis2013
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|11|29|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 11
26
+This study, DLBCL Tier 2, 29
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[ABI3BP](ABI3BP)|2 |
37
+|[CD83](CD83)|1 |
38
+|[CDH9](CDH9)|2 |
39
+|[CDKN2A](CDKN2A)|1 |
40
+|[CNTNAP5](CNTNAP5)|2 |
41
+|[DNAH5](DNAH5)|2 |
42
+|[DSG4](DSG4)|2 |
43
+|[DUSP2](DUSP2)|1 |
44
+|[FAM38B](FAM38B)|2 |
45
+|[FAT4](FAT4)|2 |
46
+|[FNDC1](FNDC1)|2 |
47
+|[GNAI2](GNAI2)|1 |
48
+|[HDAC7](HDAC7)|2 |
49
+|[HIST1H1D](HIST1H1D)|1 |
50
+|[HIST1H1E](HIST1H1E)|1 |
51
+|[HIST1H2AC](HIST1H2AC)|1 |
52
+|[HIST1H2AG](HIST1H2AG)|2 |
53
+|[IER2](IER2)|2 |
54
+|[IFNGR1](IFNGR1)|2 |
55
+|[IKZF3](IKZF3)|1 |
56
+|[LRRN3](LRRN3)|2 |
57
+|[MPDZ](MPDZ)|2 |
58
+|[MPEG1](MPEG1)|1 |
59
+|[NLRP5](NLRP5)|2 |
60
+|[ODZ3](ODZ3)|2 |
61
+|[P2RX5](P2RX5)|2 |
62
+|[PASK](PASK)|2 |
63
+|[PCDHB11](PCDHB11)|2 |
64
+|[PDS5B](PDS5B)|2 |
65
+|[PKD1](PKD1)|2 |
66
+|[POGZ](POGZ)|2 |
67
+|[PRKCB](PRKCB)|2 |
68
+|[PTPN23](PTPN23)|2 |
69
+|[RB1](RB1)|1 |
70
+|[SAMD9L](SAMD9L)|2 |
71
+|[SARM1](SARM1)|2 |
72
+|[SRRM2](SRRM2)|2 |
73
+|[SYPL1](SYPL1)|2 |
74
+|[TAF1](TAF1)|1 |
75
+|[WDFY3](WDFY3)|2 |
76
+
77
+# Details
78
+
papers/morinSomaticMutationsAltering2010a.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @morinSomaticMutationsAltering2010a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+|FL|1||
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, DLBCL Tier 1, 1
27
+This study, DLBCL Tier 2,
28
+Other DLBCL studies, DLBCL Tier 1, 128
29
+Other DLBCL studies, DLBCL Tier 2, 198
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|DLBCL tier|FL tier|
36
+|:-|:-:|:-:|
37
+|[EZH2](EZH2)|1 |1 |
38
+
39
+# Details
40
+
papers/mottokGenomicAlterationsCIITA2015b.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @mottokGenomicAlterationsCIITA2015b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[CIITA](CIITA)|1 |
37
+
38
+# Details
39
+
papers/mottokIntegrativeGenomicAnalysis2019b.md
... ...
@@ -0,0 +1,59 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @mottokIntegrativeGenomicAnalysis2019b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|6|15|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 6
26
+This study, PMBL Tier 2, 15
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[CISH](CISH)|1 |
37
+|[CXCR5](CXCR5)|2 |
38
+|[DDX3X](DDX3X)|1 |
39
+|[EPHA7](EPHA7)|2 |
40
+|[EZH2](EZH2)|1 |
41
+|[GCSAM](GCSAM)|2 |
42
+|[HIST1H2BC](HIST1H2BC)|2 |
43
+|[HIST1H4E](HIST1H4E)|2 |
44
+|[HIST1H4J](HIST1H4J)|2 |
45
+|[IL13RA1](IL13RA1)|2 |
46
+|[IL1RAPL2](IL1RAPL2)|2 |
47
+|[IRF2BP2](IRF2BP2)|2 |
48
+|[IRF4](IRF4)|2 |
49
+|[IRF8](IRF8)|1 |
50
+|[JAK1](JAK1)|1 |
51
+|[JUNB](JUNB)|2 |
52
+|[MAGEC2](MAGEC2)|2 |
53
+|[MS4A1](MS4A1)|1 |
54
+|[NFKB2](NFKB2)|2 |
55
+|[RGS1](RGS1)|2 |
56
+|[VMP1](VMP1)|2 |
57
+
58
+# Details
59
+
papers/muppidiLossSignalingGa132014b.md
... ...
@@ -0,0 +1,41 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @muppidiLossSignalingGa132014b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|1|2|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1, 1
26
+This study, BL Tier 2, 2
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[ARHGEF1](ARHGEF1)|2 |
37
+|[P2RY8](P2RY8)|1 |
38
+|[S1PR2](S1PR2)|2 |
39
+
40
+# Details
41
+
papers/nadeuGenomicEpigenomicInsights2020b.md
... ...
@@ -0,0 +1,43 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @nadeuGenomicEpigenomicInsights2020b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MCL|3|2|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MCL Tier 1, 3
26
+This study, MCL Tier 2, 2
27
+Other MCL studies, MCL Tier 1, 23
28
+Other MCL studies, MCL Tier 2, 46
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MCL tier|
35
+|:-|:-:|
36
+|[BCOR](BCOR)|2 |
37
+|[SMARCA4](SMARCA4)|1 |
38
+|[SMARCB1](SMARCB1)|2 |
39
+|[SYNE1](SYNE1)|1 |
40
+|[TERT](TERT)|1 |
41
+
42
+# Details
43
+
papers/ngoOncogenicallyActiveMYD882011a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ngoOncogenicallyActiveMYD882011a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[MYD88](MYD88)|1 |
37
+
38
+# Details
39
+
papers/ohgamiSTAT3MutationsAre2014.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ohgamiSTAT3MutationsAre2014
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[STAT3](STAT3)|1 |
37
+
38
+# Details
39
+
papers/okosunRecurrentMTORC1activatingRRAGC2016a.md
... ...
@@ -0,0 +1,42 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @okosunRecurrentMTORC1activatingRRAGC2016a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+|FL|3||
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, FL Tier 1, 3
27
+This study, FL Tier 2,
28
+Other FL studies, FL Tier 1, 66
29
+Other FL studies, FL Tier 2, 50
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|DLBCL tier|FL tier|
36
+|:-|:-:|:-:|
37
+|[ATP6AP1](ATP6AP1)| |1 |
38
+|[ATP6V1B2](ATP6V1B2)| |1 |
39
+|[RRAGC](RRAGC)|1 |1 |
40
+
41
+# Details
42
+
papers/oricchioGeneticEpigeneticInactivation2017b.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @oricchioGeneticEpigeneticInactivation2017b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL||1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, FL Tier 1,
26
+This study, FL Tier 2, 1
27
+Other FL studies, FL Tier 1, 66
28
+Other FL studies, FL Tier 2, 50
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|FL tier|
35
+|:-|:-:|
36
+|[SESN1](SESN1)|2 |
37
+
38
+# Details
39
+
papers/ottoGeneticLesionsTRAF32012a.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ottoGeneticLesionsTRAF32012a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|2||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 2
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[MAP3K14](MAP3K14)|1 |
37
+|[TRAF3](TRAF3)|1 |
38
+
39
+# Details
40
+
papers/paneaWholeGenomeLandscape2019.md
... ...
@@ -0,0 +1,90 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @paneaWholeGenomeLandscape2019
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|4|46|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: left
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 4
26
+New Tier 1, BL Tier 1, 4
27
+This study, New Tier 2, 46
28
+New Tier 2, BL Tier 2, 46
29
+Other BL studies, BL Tier 1, 29
30
+Other BL studies, BL Tier 2, 157
31
+```
32
+
33
+
34
+## Novel genes reported in this study
35
+
36
+|New gene|BL tier|
37
+|:-|:-:|
38
+|[ALPK2](ALPK2)|2 |
39
+|[BMP7](BMP7)|1 |
40
+|[CARD11](CARD11)|2 |
41
+|[CD79B](CD79B)|2 |
42
+|[CD83](CD83)|2 |
43
+|[CTCF](CTCF)|2 |
44
+|[CXCR4](CXCR4)|2 |
45
+|[DNMT1](DNMT1)|2 |
46
+|[DTX1](DTX1)|2 |
47
+|[EIF4A1](EIF4A1)|1 |
48
+|[EP300](EP300)|2 |
49
+|[EPPK1](EPPK1)|1 |
50
+|[ETS1](ETS1)|2 |
51
+|[FZD3](FZD3)|2 |
52
+|[GRB2](GRB2)|2 |
53
+|[HIST1H1C](HIST1H1C)|2 |
54
+|[HIST1H2AG](HIST1H2AG)|2 |
55
+|[HIST1H2AM](HIST1H2AM)|2 |
56
+|[HIST1H2BK](HIST1H2BK)|2 |
57
+|[HIST1H3D](HIST1H3D)|2 |
58
+|[HIST1H3H](HIST1H3H)|2 |
59
+|[HIST1H3I](HIST1H3I)|2 |
60
+|[HIST1H3J](HIST1H3J)|2 |
61
+|[HIST1H4J](HIST1H4J)|2 |
62
+|[HNRNPU](HNRNPU)|1 |
63
+|[IGLL5](IGLL5)|2 |
64
+|[IKZF3](IKZF3)|2 |
65
+|[IRF8](IRF8)|2 |
66
+|[KCNK10](KCNK10)|2 |
67
+|[KLHL6](KLHL6)|2 |
68
+|[LTB](LTB)|2 |
69
+|[MCL1](MCL1)|2 |
70
+|[MME](MME)|2 |
71
+|[MTOR](MTOR)|2 |
72
+|[NOTCH2](NOTCH2)|2 |
73
+|[PABPC4L](PABPC4L)|2 |
74
+|[PCDHA11](PCDHA11)|2 |
75
+|[PDZRN3](PDZRN3)|2 |
76
+|[PIK3R1](PIK3R1)|2 |
77
+|[PLCG2](PLCG2)|2 |
78
+|[PXDNL](PXDNL)|2 |
79
+|[RAC2](RAC2)|2 |
80
+|[RNF144B](RNF144B)|2 |
81
+|[SNTB2](SNTB2)|2 |
82
+|[SP3](SP3)|2 |
83
+|[SYNCRIP](SYNCRIP)|2 |
84
+|[TET2](TET2)|2 |
85
+|[WDR7](WDR7)|2 |
86
+|[WNK2](WNK2)|2 |
87
+|[ZFP36L1](ZFP36L1)|2 |
88
+
89
+# Details
90
+
papers/pararajalingamCodingNoncodingDrivers2020.md
... ...
@@ -0,0 +1,46 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pararajalingamCodingNoncodingDrivers2020
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MCL|6|1|
12
+|DLBCL|2|3|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, MCL Tier 1, 6
27
+This study, MCL Tier 2, 1
28
+Other MCL studies, MCL Tier 1, 23
29
+Other MCL studies, MCL Tier 2, 46
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|MCL tier|DLBCL tier|
36
+|:-|:-:|:-:|
37
+|[B2M](B2M)|2 |1 |
38
+|[DAZAP1](DAZAP1)|1 |2 |
39
+|[EWSR1](EWSR1)|1 | |
40
+|[HNRNPH1](HNRNPH1)|1 |2 |
41
+|[NFKBIE](NFKBIE)|1 |1 |
42
+|[S1PR1](S1PR1)|1 | |
43
+|[UBR5](UBR5)|1 |2 |
44
+
45
+# Details
46
+
papers/parryWholeExomeSequencing2013.md
... ...
@@ -0,0 +1,47 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @parryWholeExomeSequencing2013
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL||8|
12
+|DLBCL|3|1|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, MZL Tier 1,
27
+This study, MZL Tier 2, 8
28
+Other MZL studies, MZL Tier 1, 42
29
+Other MZL studies, MZL Tier 2, 74
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|MZL tier|DLBCL tier|
36
+|:-|:-:|:-:|
37
+|[AMOTL1](AMOTL1)|2 | |
38
+|[CBFA2T3](CBFA2T3)|2 | |
39
+|[CREBBP](CREBBP)|2 |1 |
40
+|[FAT4](FAT4)|2 |2 |
41
+|[FBXO11](FBXO11)|2 |1 |
42
+|[PLA2G4D](PLA2G4D)|2 | |
43
+|[TRRAP](TRRAP)|2 |1 |
44
+|[USH2A](USH2A)|2 | |
45
+
46
+# Details
47
+
papers/pasqualucciAnalysisCodingGenome2011.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pasqualucciAnalysisCodingGenome2011
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|3|4|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 3
26
+This study, DLBCL Tier 2, 4
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[CD36](CD36)|2 |
37
+|[GRB2](GRB2)|1 |
38
+|[HNF1B](HNF1B)|2 |
39
+|[KLF2](KLF2)|1 |
40
+|[MYOM2](MYOM2)|2 |
41
+|[NOTCH1](NOTCH1)|1 |
42
+|[TRAF3](TRAF3)|2 |
43
+
44
+# Details
45
+
papers/pasqualucciHypermutationMultipleProtooncogenes2001a.md
... ...
@@ -0,0 +1,42 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pasqualucciHypermutationMultipleProtooncogenes2001a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|2|2|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 2
26
+This study, DLBCL Tier 2, 2
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[MYC](MYC)|1 |
37
+|[PAX5](PAX5)|2 |
38
+|[PIM1](PIM1)|1 |
39
+|[RHOH](RHOH)|2 |
40
+
41
+# Details
42
+
papers/pasqualucciInactivatingMutationsAcetyltransferase2011a.md
... ...
@@ -0,0 +1,41 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pasqualucciInactivatingMutationsAcetyltransferase2011a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|2||
12
+|DLBCL|2||
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, FL Tier 1, 2
27
+This study, FL Tier 2,
28
+Other FL studies, FL Tier 1, 66
29
+Other FL studies, FL Tier 2, 50
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|FL tier|DLBCL tier|
36
+|:-|:-:|:-:|
37
+|[CREBBP](CREBBP)|1 |1 |
38
+|[EP300](EP300)|1 |1 |
39
+
40
+# Details
41
+
papers/pasqualucciInactivationPRDM1BLIMP12006a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @pasqualucciInactivationPRDM1BLIMP12006a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[PRDM1](PRDM1)|1 |
37
+
38
+# Details
39
+
papers/reddyGeneticFunctionalDrivers2017.md
... ...
@@ -0,0 +1,98 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @reddyGeneticFunctionalDrivers2017
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|7|53|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 7
26
+This study, DLBCL Tier 2, 53
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[ANKRD17](ANKRD17)|2 |
37
+|[ARID1B](ARID1B)|2 |
38
+|[ARID5B](ARID5B)|2 |
39
+|[ATM](ATM)|1 |
40
+|[ATR](ATR)|2 |
41
+|[BIRC6](BIRC6)|1 |
42
+|[BRINP3](BRINP3)|2 |
43
+|[BTBD3](BTBD3)|2 |
44
+|[CASP8](CASP8)|2 |
45
+|[CBLB](CBLB)|2 |
46
+|[CD22](CD22)|2 |
47
+|[CDC73](CDC73)|2 |
48
+|[CHD1](CHD1)|2 |
49
+|[CHD8](CHD8)|2 |
50
+|[CHST2](CHST2)|2 |
51
+|[DCAF6](DCAF6)|2 |
52
+|[DDX10](DDX10)|2 |
53
+|[DICER1](DICER1)|2 |
54
+|[DNMT3A](DNMT3A)|2 |
55
+|[FOXP1](FOXP1)|2 |
56
+|[FUBP1](FUBP1)|2 |
57
+|[GNAS](GNAS)|2 |
58
+|[GOLGA5](GOLGA5)|2 |
59
+|[HIST1H2BC](HIST1H2BC)|1 |
60
+|[HNRNPU](HNRNPU)|1 |
61
+|[HRAS](HRAS)|2 |
62
+|[IKBKB](IKBKB)|2 |
63
+|[JUNB](JUNB)|2 |
64
+|[KCMF1](KCMF1)|2 |
65
+|[LIN54](LIN54)|2 |
66
+|[MAGT1](MAGT1)|2 |
67
+|[MAP4K4](MAP4K4)|2 |
68
+|[MARK1](MARK1)|2 |
69
+|[MCL1](MCL1)|2 |
70
+|[MECOM](MECOM)|2 |
71
+|[MET](MET)|2 |
72
+|[MSH2](MSH2)|2 |
73
+|[MSH6](MSH6)|2 |
74
+|[MYB](MYB)|2 |
75
+|[NCOR1](NCOR1)|2 |
76
+|[NF1](NF1)|2 |
77
+|[NFKB2](NFKB2)|2 |
78
+|[PHF6](PHF6)|2 |
79
+|[PIK3CD](PIK3CD)|2 |
80
+|[PTPN6](PTPN6)|2 |
81
+|[PTPRK](PTPRK)|2 |
82
+|[RARA](RARA)|2 |
83
+|[RUNX1](RUNX1)|2 |
84
+|[SETD1B](SETD1B)|1 |
85
+|[SETD5](SETD5)|2 |
86
+|[SYK](SYK)|2 |
87
+|[TGFBR2](TGFBR2)|2 |
88
+|[TIPARP](TIPARP)|2 |
89
+|[TOX](TOX)|1 |
90
+|[UBE2A](UBE2A)|1 |
91
+|[WAC](WAC)|2 |
92
+|[YY1](YY1)|2 |
93
+|[ZBTB7A](ZBTB7A)|2 |
94
+|[ZFAT](ZFAT)|2 |
95
+|[ZFX](ZFX)|2 |
96
+
97
+# Details
98
+
papers/reichelFlowSortingExome2015a.md
... ...
@@ -0,0 +1,67 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @reichelFlowSortingExome2015a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|11|18|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 11
26
+This study, PMBL Tier 2, 18
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[ARIH2](ARIH2)|2 |
37
+|[B2M](B2M)|1 |
38
+|[BCL7A](BCL7A)|2 |
39
+|[CSF2RB](CSF2RB)|1 |
40
+|[DMD](DMD)|2 |
41
+|[EBF1](EBF1)|1 |
42
+|[EEF1A1](EEF1A1)|1 |
43
+|[EGR1](EGR1)|2 |
44
+|[GNA13](GNA13)|1 |
45
+|[HECW2](HECW2)|2 |
46
+|[HELLS](HELLS)|2 |
47
+|[HIST1H1E](HIST1H1E)|1 |
48
+|[HIST1H3B](HIST1H3B)|2 |
49
+|[HIST1H4C](HIST1H4C)|2 |
50
+|[ITPKB](ITPKB)|1 |
51
+|[MPDZ](MPDZ)|2 |
52
+|[NEK1](NEK1)|2 |
53
+|[PIM2](PIM2)|1 |
54
+|[RANBP2](RANBP2)|2 |
55
+|[SENP7](SENP7)|2 |
56
+|[SETDB1](SETDB1)|2 |
57
+|[SIAH2](SIAH2)|2 |
58
+|[TBC1D15](TBC1D15)|2 |
59
+|[TICRR](TICRR)|2 |
60
+|[TRIP11](TRIP11)|2 |
61
+|[UBE2A](UBE2A)|1 |
62
+|[WEE1](WEE1)|1 |
63
+|[ZFP36L1](ZFP36L1)|1 |
64
+|[ZNF217](ZNF217)|2 |
65
+
66
+# Details
67
+
papers/richterRecurrentMutationID32012a.md
... ...
@@ -0,0 +1,43 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @richterRecurrentMutationID32012a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|5||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1, 5
26
+This study, BL Tier 2,
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[CCND3](CCND3)|1 |
37
+|[FBXO11](FBXO11)|1 |
38
+|[ID3](ID3)|1 |
39
+|[RHOA](RHOA)|1 |
40
+|[SMARCA4](SMARCA4)|1 |
41
+
42
+# Details
43
+
papers/ritzRecurrentMutationsSTAT62009a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @ritzRecurrentMutationsSTAT62009a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[STAT6](STAT6)|1 |
37
+
38
+# Details
39
+
papers/rossiAlterationBIRC3Multiple2011a.md
... ...
@@ -0,0 +1,43 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @rossiAlterationBIRC3Multiple2011a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL|4|1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MZL Tier 1, 4
26
+This study, MZL Tier 2, 1
27
+Other MZL studies, MZL Tier 1, 42
28
+Other MZL studies, MZL Tier 2, 74
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MZL tier|
35
+|:-|:-:|
36
+|[BIRC3](BIRC3)|1 |
37
+|[IKBKB](IKBKB)|2 |
38
+|[MAP3K14](MAP3K14)|1 |
39
+|[TNFAIP3](TNFAIP3)|1 |
40
+|[TRAF3](TRAF3)|1 |
41
+
42
+# Details
43
+
papers/rossiCodingGenomeSplenic2012c.md
... ...
@@ -0,0 +1,60 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @rossiCodingGenomeSplenic2012c
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|12|2|
12
+|MZL|10|11|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, MZL Tier 1, 10
27
+This study, MZL Tier 2, 11
28
+Other MZL studies, MZL Tier 1, 42
29
+Other MZL studies, MZL Tier 2, 74
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|DLBCL tier|MZL tier|
36
+|:-|:-:|:-:|
37
+|[ARID1A](ARID1A)|1 |1 |
38
+|[CD79A](CD79A)| |2 |
39
+|[DTX1](DTX1)|1 |1 |
40
+|[EGR1](EGR1)| |2 |
41
+|[EGR2](EGR2)| |2 |
42
+|[EP300](EP300)|1 |1 |
43
+|[GPS2](GPS2)| |2 |
44
+|[HIST1H2AG](HIST1H2AG)|2 |2 |
45
+|[HIST1H2BK](HIST1H2BK)|1 |2 |
46
+|[KMT2D](KMT2D)|1 |1 |
47
+|[MCRS1](MCRS1)| |2 |
48
+|[MSL2](MSL2)| |2 |
49
+|[NOTCH1](NOTCH1)|1 |1 |
50
+|[NOTCH2](NOTCH2)|1 |1 |
51
+|[SIN3A](SIN3A)|1 |1 |
52
+|[SPEN](SPEN)|1 |1 |
53
+|[SWAP70](SWAP70)| |2 |
54
+|[TBL1XR1](TBL1XR1)|1 |1 |
55
+|[TP53](TP53)|1 |1 |
56
+|[TRRAP](TRRAP)|1 |2 |
57
+|[WAC](WAC)|2 |2 |
58
+
59
+# Details
60
+
papers/rushtonGeneticEvolutionaryPatterns2020.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @rushtonGeneticEvolutionaryPatterns2020
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[MS4A1](MS4A1)|1 |
37
+
38
+# Details
39
+
papers/russler-germainMutationsAssociatedProgression2023b.md
... ...
@@ -0,0 +1,58 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @russler-germainMutationsAssociatedProgression2023b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|1|19|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, FL Tier 1, 1
26
+This study, FL Tier 2, 19
27
+Other FL studies, FL Tier 1, 66
28
+Other FL studies, FL Tier 2, 50
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|FL tier|
35
+|:-|:-:|
36
+|[ABL2](ABL2)|2 |
37
+|[BCL10](BCL10)|2 |
38
+|[CD70](CD70)|2 |
39
+|[CD83](CD83)|1 |
40
+|[CILP](CILP)|2 |
41
+|[CYP2A6](CYP2A6)|2 |
42
+|[GBP7](GBP7)|2 |
43
+|[GRM6](GRM6)|2 |
44
+|[IGLL5](IGLL5)|2 |
45
+|[KIR3DL1](KIR3DL1)|2 |
46
+|[MAGEC1](MAGEC1)|2 |
47
+|[MAP7D1](MAP7D1)|2 |
48
+|[MKI67](MKI67)|2 |
49
+|[NFKBIA](NFKBIA)|2 |
50
+|[OR8H2](OR8H2)|2 |
51
+|[PZP](PZP)|2 |
52
+|[SHROOM3](SHROOM3)|2 |
53
+|[SRRM2](SRRM2)|2 |
54
+|[STAB2](STAB2)|2 |
55
+|[XIRP2](XIRP2)|2 |
56
+
57
+# Details
58
+
papers/sarkozyMutationalLandscapeGray2021a.md
... ...
@@ -0,0 +1,49 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @sarkozyMutationalLandscapeGray2021a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|5|6|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 5
26
+This study, PMBL Tier 2, 6
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[ABCA13](ABCA13)|2 |
37
+|[BCL2](BCL2)|2 |
38
+|[BIRC6](BIRC6)|1 |
39
+|[BTG1](BTG1)|1 |
40
+|[HIST1H1B](HIST1H1B)|1 |
41
+|[KMT2C](KMT2C)|1 |
42
+|[LRRN3](LRRN3)|2 |
43
+|[MFHAS1](MFHAS1)|2 |
44
+|[NCOR2](NCOR2)|2 |
45
+|[RELN](RELN)|2 |
46
+|[SPEN](SPEN)|1 |
47
+
48
+# Details
49
+
papers/schmitzBurkittLymphomaPathogenesis2012.md
... ...
@@ -0,0 +1,59 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schmitzBurkittLymphomaPathogenesis2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|4|16|
12
+|DLBCL|2|3|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, BL Tier 1, 4
27
+This study, BL Tier 2, 16
28
+Other BL studies, BL Tier 1, 29
29
+Other BL studies, BL Tier 2, 157
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|BL tier|DLBCL tier|
36
+|:-|:-:|:-:|
37
+|[C16orf48](C16orf48)|2 | |
38
+|[DDX3X](DDX3X)|1 |1 |
39
+|[DHCR7](DHCR7)|2 | |
40
+|[ELP2](ELP2)|2 | |
41
+|[EXOSC6](EXOSC6)|2 | |
42
+|[FLYWCH1](FLYWCH1)|2 | |
43
+|[FOXO1](FOXO1)|1 |1 |
44
+|[GTSE1](GTSE1)|2 | |
45
+|[ID3](ID3)|1 |2 |
46
+|[KANK2](KANK2)|2 | |
47
+|[MKI67](MKI67)|2 | |
48
+|[MYO18A](MYO18A)|2 | |
49
+|[NCOR2](NCOR2)|2 |2 |
50
+|[PCBP1](PCBP1)|2 |2 |
51
+|[PDCD11](PDCD11)|2 | |
52
+|[TCF3](TCF3)|1 | |
53
+|[TOP2A](TOP2A)|2 | |
54
+|[WDR90](WDR90)|2 | |
55
+|[WHAMM](WHAMM)|2 | |
56
+|[YY1AP1](YY1AP1)|2 | |
57
+
58
+# Details
59
+
papers/schmitzGeneticsPathogenesisDiffuse2018a.md
... ...
@@ -0,0 +1,54 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schmitzGeneticsPathogenesisDiffuse2018a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|7|9|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 7
26
+This study, DLBCL Tier 2, 9
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[CXCR5](CXCR5)|1 |
37
+|[DDX3X](DDX3X)|1 |
38
+|[DTX1](DTX1)|1 |
39
+|[FOXC1](FOXC1)|2 |
40
+|[GPC5](GPC5)|2 |
41
+|[GSG2](GSG2)|2 |
42
+|[HIST2H2BE](HIST2H2BE)|1 |
43
+|[ITPKB](ITPKB)|1 |
44
+|[KLHL21](KLHL21)|2 |
45
+|[LAMA5](LAMA5)|2 |
46
+|[MYBPC2](MYBPC2)|2 |
47
+|[NOL9](NOL9)|1 |
48
+|[PAPOLG](PAPOLG)|2 |
49
+|[PRKDC](PRKDC)|2 |
50
+|[TAP1](TAP1)|2 |
51
+|[WEE1](WEE1)|1 |
52
+
53
+# Details
54
+
papers/schmitzTNFAIP3A20Tumor2009a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schmitzTNFAIP3A20Tumor2009a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[TNFAIP3](TNFAIP3)|1 |
37
+
38
+# Details
39
+
papers/schneiderAlterationsCD58Gene2015a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schneiderAlterationsCD58Gene2015a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[CD58](CD58)|1 |
37
+
38
+# Details
39
+
papers/schollMutationsRegionFAS2007.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @schollMutationsRegionFAS2007
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[FAS](FAS)|1 |
37
+
38
+# Details
39
+
papers/shinBRAFV600EMAP2K12015.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @shinBRAFV600EMAP2K12015
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL||1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1,
26
+This study, DLBCL Tier 2, 1
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[MAP2K1](MAP2K1)|2 |
37
+
38
+# Details
39
+
papers/spinaGeneticsNodalMarginal2016b.md
... ...
@@ -0,0 +1,69 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @spinaGeneticsNodalMarginal2016b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL|8|23|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MZL Tier 1, 8
26
+This study, MZL Tier 2, 23
27
+Other MZL studies, MZL Tier 1, 42
28
+Other MZL studies, MZL Tier 2, 74
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MZL tier|
35
+|:-|:-:|
36
+|[ABCA13](ABCA13)|2 |
37
+|[ACTG1](ACTG1)|2 |
38
+|[ADD2](ADD2)|2 |
39
+|[AMN](AMN)|2 |
40
+|[AOC2](AOC2)|2 |
41
+|[BCL10](BCL10)|1 |
42
+|[C6orf103](C6orf103)|2 |
43
+|[CDC42BPB](CDC42BPB)|2 |
44
+|[CDKN2A](CDKN2A)|2 |
45
+|[CLGN](CLGN)|2 |
46
+|[CNKSR2](CNKSR2)|2 |
47
+|[FAS](FAS)|1 |
48
+|[FAT1](FAT1)|1 |
49
+|[GPR98](GPR98)|2 |
50
+|[ID3](ID3)|1 |
51
+|[LRP1B](LRP1B)|2 |
52
+|[NCOR2](NCOR2)|1 |
53
+|[NOL9](NOL9)|1 |
54
+|[PACRG](PACRG)|2 |
55
+|[PARK2](PARK2)|2 |
56
+|[PLXNB3](PLXNB3)|2 |
57
+|[PTPRD](PTPRD)|1 |
58
+|[RCOR1](RCOR1)|2 |
59
+|[RPL1L](RPL1L)|2 |
60
+|[SAMD5](SAMD5)|2 |
61
+|[SCG3](SCG3)|2 |
62
+|[STXBP5](STXBP5)|2 |
63
+|[TAF1](TAF1)|2 |
64
+|[TCTN2](TCTN2)|2 |
65
+|[TNFRSF14](TNFRSF14)|1 |
66
+|[ZNF9](ZNF9)|2 |
67
+
68
+# Details
69
+
papers/tanakaFrequentIncidenceSomatic1992.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @tanakaFrequentIncidenceSomatic1992
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[BCL2](BCL2)|1 |
37
+
38
+# Details
39
+
papers/thomasGeneticSubgroupsInform2023.md
... ...
@@ -0,0 +1,43 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @thomasGeneticSubgroupsInform2023
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|2|3|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1, 2
26
+This study, BL Tier 2, 3
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[CDKN2C](CDKN2C)|2 |
37
+|[EBF1](EBF1)|2 |
38
+|[EHD1](EHD1)|2 |
39
+|[PHF6](PHF6)|1 |
40
+|[WNK1](WNK1)|1 |
41
+
42
+# Details
43
+
papers/tiacciBRAFMutationsHairycell2011a.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @tiacciBRAFMutationsHairycell2011a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[BRAF](BRAF)|1 |
37
+
38
+# Details
39
+
papers/tiacciPervasiveMutationsJAKSTAT2018b.md
... ...
@@ -0,0 +1,48 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @tiacciPervasiveMutationsJAKSTAT2018b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1|9|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2, 9
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[AKAP6](AKAP6)|2 |
37
+|[DGKB](DGKB)|2 |
38
+|[ITPR3](ITPR3)|2 |
39
+|[NUP214](NUP214)|2 |
40
+|[PRUNE2](PRUNE2)|2 |
41
+|[SETD5](SETD5)|2 |
42
+|[STAT5B](STAT5B)|2 |
43
+|[TNIP1](TNIP1)|2 |
44
+|[TP53](TP53)|1 |
45
+|[ZCCHC11](ZCCHC11)|2 |
46
+
47
+# Details
48
+
papers/troenNOTCH2MutationsMarginal2008.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @troenNOTCH2MutationsMarginal2008
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 1
26
+This study, DLBCL Tier 2,
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[NOTCH2](NOTCH2)|1 |
37
+
38
+# Details
39
+
papers/vandenbrandRecurrentMutationsGenes2017.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @vandenbrandRecurrentMutationsGenes2017
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL||2|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MZL Tier 1,
26
+This study, MZL Tier 2, 2
27
+Other MZL studies, MZL Tier 1, 42
28
+Other MZL studies, MZL Tier 2, 74
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MZL tier|
35
+|:-|:-:|
36
+|[CD9B](CD9B)|2 |
37
+|[TNIP2](TNIP2)|2 |
38
+
39
+# Details
40
+
papers/viganoSomaticIL4RMutations2018b.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @viganoSomaticIL4RMutations2018b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2,
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[IL4R](IL4R)|1 |
37
+
38
+# Details
39
+
papers/wenigerMutationsTumorSuppressor2006a.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @wenigerMutationsTumorSuppressor2006a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1|1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 1
26
+This study, PMBL Tier 2, 1
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[GPR126](GPR126)|2 |
37
+|[SOCS1](SOCS1)|1 |
38
+
39
+# Details
40
+
papers/wienandGenomicAnalysesFlowsorted2019b.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @wienandGenomicAnalysesFlowsorted2019b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|4|3|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, PMBL Tier 1, 4
26
+This study, PMBL Tier 2, 3
27
+Other PMBL studies, PMBL Tier 1, 76
28
+Other PMBL studies, PMBL Tier 2, 82
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|PMBL tier|
35
+|:-|:-:|
36
+|[ACTB](ACTB)|1 |
37
+|[ARID1A](ARID1A)|1 |
38
+|[DNAH12](DNAH12)|2 |
39
+|[HLA-B](HLA-B)|1 |
40
+|[IKBKB](IKBKB)|2 |
41
+|[NFKBIA](NFKBIA)|1 |
42
+|[RBM38](RBM38)|2 |
43
+
44
+# Details
45
+
papers/wildaInactivationARFMDM2p53Pathway2004.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @wildaInactivationARFMDM2p53Pathway2004
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1, 1
26
+This study, BL Tier 2,
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[TP53](TP53)|1 |
37
+
38
+# Details
39
+
papers/wuGeneticHeterogeneityPrimary2016.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @wuGeneticHeterogeneityPrimary2016
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MCL|1||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MCL Tier 1, 1
26
+This study, MCL Tier 2,
27
+Other MCL studies, MCL Tier 1, 23
28
+Other MCL studies, MCL Tier 2, 46
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MCL tier|
35
+|:-|:-:|
36
+|[CARD11](CARD11)|1 |
37
+
38
+# Details
39
+
papers/yanBCRTLRSignaling2012a.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @yanBCRTLRSignaling2012a
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MZL|2||
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MZL Tier 1, 2
26
+This study, MZL Tier 2,
27
+Other MZL studies, MZL Tier 1, 42
28
+Other MZL studies, MZL Tier 2, 74
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MZL tier|
35
+|:-|:-:|
36
+|[CARD11](CARD11)|1 |
37
+|[MYD88](MYD88)|1 |
38
+
39
+# Details
40
+
papers/yildizActivatingSTAT6Mutations2015c.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @yildizActivatingSTAT6Mutations2015c
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|1||
12
+|DLBCL|1||
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 300
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, DLBCL Tier 1, 1
27
+This study, DLBCL Tier 2,
28
+Other DLBCL studies, DLBCL Tier 1, 128
29
+Other DLBCL studies, DLBCL Tier 2, 198
30
+```
31
+
32
+
33
+## Novel genes reported in this study
34
+
35
+|New gene|FL tier|DLBCL tier|
36
+|:-|:-:|:-:|
37
+|[STAT6](STAT6)|1 |1 |
38
+
39
+# Details
40
+
papers/zhangGeneticHeterogeneityDiffuse2013.md
... ...
@@ -0,0 +1,57 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @zhangGeneticHeterogeneityDiffuse2013
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|11|8|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, DLBCL Tier 1, 11
26
+This study, DLBCL Tier 2, 8
27
+Other DLBCL studies, DLBCL Tier 1, 128
28
+Other DLBCL studies, DLBCL Tier 2, 198
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[ARID1A](ARID1A)|1 |
37
+|[FBXW7](FBXW7)|1 |
38
+|[HIST1H3B](HIST1H3B)|1 |
39
+|[INO80](INO80)|2 |
40
+|[JAK1](JAK1)|2 |
41
+|[JAK3](JAK3)|2 |
42
+|[KLHL14](KLHL14)|1 |
43
+|[KMT2C](KMT2C)|1 |
44
+|[MGA](MGA)|1 |
45
+|[MTOR](MTOR)|1 |
46
+|[PIK3R1](PIK3R1)|2 |
47
+|[POU2F2](POU2F2)|1 |
48
+|[SETD2](SETD2)|2 |
49
+|[SMARCA4](SMARCA4)|1 |
50
+|[STAT5B](STAT5B)|2 |
51
+|[UBR5](UBR5)|2 |
52
+|[ZEB2](ZEB2)|2 |
53
+|[ZNF292](ZNF292)|1 |
54
+|[ZNF608](ZNF608)|1 |
55
+
56
+# Details
57
+
papers/zhangGenomicLandscapeMantle2014.md
... ...
@@ -0,0 +1,66 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @zhangGenomicLandscapeMantle2014
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MCL|2|26|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, MCL Tier 1, 2
26
+This study, MCL Tier 2, 26
27
+Other MCL studies, MCL Tier 1, 23
28
+Other MCL studies, MCL Tier 2, 46
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|MCL tier|
35
+|:-|:-:|
36
+|[ANK2](ANK2)|2 |
37
+|[ATP11C](ATP11C)|2 |
38
+|[CDH8](CDH8)|2 |
39
+|[COL11A1](COL11A1)|2 |
40
+|[COL16A1](COL16A1)|2 |
41
+|[CTNNA2](CTNNA2)|2 |
42
+|[DHDH](DHDH)|2 |
43
+|[DLC1](DLC1)|2 |
44
+|[EIF2AK4](EIF2AK4)|2 |
45
+|[ESX1](ESX1)|2 |
46
+|[FAT4](FAT4)|2 |
47
+|[GRIN2A](GRIN2A)|2 |
48
+|[HEPH](HEPH)|2 |
49
+|[KMT2C](KMT2C)|2 |
50
+|[MRGPRF](MRGPRF)|2 |
51
+|[NIN](NIN)|2 |
52
+|[OGDHL](OGDHL)|2 |
53
+|[PCDHB2](PCDHB2)|2 |
54
+|[PLXNB3](PLXNB3)|2 |
55
+|[POT1](POT1)|1 |
56
+|[RB1](RB1)|1 |
57
+|[ROBO2](ROBO2)|2 |
58
+|[SALL3](SALL3)|2 |
59
+|[SI](SI)|2 |
60
+|[SMC1A](SMC1A)|2 |
61
+|[TBC1D26](TBC1D26)|2 |
62
+|[ZNF117](ZNF117)|2 |
63
+|[ZNF296](ZNF296)|2 |
64
+
65
+# Details
66
+
papers/zhouSporadicEndemicBurkitt2019.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @zhouSporadicEndemicBurkitt2019
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL||1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 300
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, BL Tier 1,
26
+This study, BL Tier 2, 1
27
+Other BL studies, BL Tier 1, 29
28
+Other BL studies, BL Tier 2, 157
29
+```
30
+
31
+
32
+## Novel genes reported in this study
33
+
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[KMT2C](KMT2C)|2 |
37
+
38
+# Details
39
+
pararajalingamCodingNoncodingDrivers2020.md
... ...
@@ -1,46 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pararajalingamCodingNoncodingDrivers2020
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|6|1|
12
-|DLBCL|2|3|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, MCL Tier 1, 6
27
-This study, MCL Tier 2, 1
28
-Other MCL studies, MCL Tier 1, 23
29
-Other MCL studies, MCL Tier 2, 46
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|MCL tier|DLBCL tier|
36
-|:-|:-:|:-:|
37
-|[B2M](B2M)|2 |1 |
38
-|[DAZAP1](DAZAP1)|1 |2 |
39
-|[EWSR1](EWSR1)|1 | |
40
-|[HNRNPH1](HNRNPH1)|1 |2 |
41
-|[NFKBIE](NFKBIE)|1 |1 |
42
-|[S1PR1](S1PR1)|1 | |
43
-|[UBR5](UBR5)|1 |2 |
44
-
45
-# Details
46
-
parryWholeExomeSequencing2013.md
... ...
@@ -1,47 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @parryWholeExomeSequencing2013
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL||8|
12
-|DLBCL|3|1|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, MZL Tier 1,
27
-This study, MZL Tier 2, 8
28
-Other MZL studies, MZL Tier 1, 42
29
-Other MZL studies, MZL Tier 2, 74
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|MZL tier|DLBCL tier|
36
-|:-|:-:|:-:|
37
-|[AMOTL1](AMOTL1)|2 | |
38
-|[CBFA2T3](CBFA2T3)|2 | |
39
-|[CREBBP](CREBBP)|2 |1 |
40
-|[FAT4](FAT4)|2 |2 |
41
-|[FBXO11](FBXO11)|2 |1 |
42
-|[PLA2G4D](PLA2G4D)|2 | |
43
-|[TRRAP](TRRAP)|2 |1 |
44
-|[USH2A](USH2A)|2 | |
45
-
46
-# Details
47
-
pasqualucciAnalysisCodingGenome2011.md
... ...
@@ -1,45 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pasqualucciAnalysisCodingGenome2011
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|4|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 3
26
-This study, DLBCL Tier 2, 4
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[CD36](CD36)|2 |
37
-|[GRB2](GRB2)|1 |
38
-|[HNF1B](HNF1B)|2 |
39
-|[KLF2](KLF2)|1 |
40
-|[MYOM2](MYOM2)|2 |
41
-|[NOTCH1](NOTCH1)|1 |
42
-|[TRAF3](TRAF3)|2 |
43
-
44
-# Details
45
-
pasqualucciHypermutationMultipleProtooncogenes2001a.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pasqualucciHypermutationMultipleProtooncogenes2001a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 2
26
-This study, DLBCL Tier 2, 2
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[MYC](MYC)|1 |
37
-|[PAX5](PAX5)|2 |
38
-|[PIM1](PIM1)|1 |
39
-|[RHOH](RHOH)|2 |
40
-
41
-# Details
42
-
pasqualucciInactivatingMutationsAcetyltransferase2011a.md
... ...
@@ -1,41 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pasqualucciInactivatingMutationsAcetyltransferase2011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|2||
12
-|DLBCL|2||
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, FL Tier 1, 2
27
-This study, FL Tier 2,
28
-Other FL studies, FL Tier 1, 66
29
-Other FL studies, FL Tier 2, 50
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|FL tier|DLBCL tier|
36
-|:-|:-:|:-:|
37
-|[CREBBP](CREBBP)|1 |1 |
38
-|[EP300](EP300)|1 |1 |
39
-
40
-# Details
41
-
pasqualucciInactivationPRDM1BLIMP12006a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @pasqualucciInactivationPRDM1BLIMP12006a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[PRDM1](PRDM1)|1 |
37
-
38
-# Details
39
-
reddyGeneticFunctionalDrivers2017.md
... ...
@@ -1,98 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @reddyGeneticFunctionalDrivers2017
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|7|53|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 7
26
-This study, DLBCL Tier 2, 53
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[ANKRD17](ANKRD17)|2 |
37
-|[ARID1B](ARID1B)|2 |
38
-|[ARID5B](ARID5B)|2 |
39
-|[ATM](ATM)|1 |
40
-|[ATR](ATR)|2 |
41
-|[BIRC6](BIRC6)|1 |
42
-|[BRINP3](BRINP3)|2 |
43
-|[BTBD3](BTBD3)|2 |
44
-|[CASP8](CASP8)|2 |
45
-|[CBLB](CBLB)|2 |
46
-|[CD22](CD22)|2 |
47
-|[CDC73](CDC73)|2 |
48
-|[CHD1](CHD1)|2 |
49
-|[CHD8](CHD8)|2 |
50
-|[CHST2](CHST2)|2 |
51
-|[DCAF6](DCAF6)|2 |
52
-|[DDX10](DDX10)|2 |
53
-|[DICER1](DICER1)|2 |
54
-|[DNMT3A](DNMT3A)|2 |
55
-|[FOXP1](FOXP1)|2 |
56
-|[FUBP1](FUBP1)|2 |
57
-|[GNAS](GNAS)|2 |
58
-|[GOLGA5](GOLGA5)|2 |
59
-|[HIST1H2BC](HIST1H2BC)|1 |
60
-|[HNRNPU](HNRNPU)|1 |
61
-|[HRAS](HRAS)|2 |
62
-|[IKBKB](IKBKB)|2 |
63
-|[JUNB](JUNB)|2 |
64
-|[KCMF1](KCMF1)|2 |
65
-|[LIN54](LIN54)|2 |
66
-|[MAGT1](MAGT1)|2 |
67
-|[MAP4K4](MAP4K4)|2 |
68
-|[MARK1](MARK1)|2 |
69
-|[MCL1](MCL1)|2 |
70
-|[MECOM](MECOM)|2 |
71
-|[MET](MET)|2 |
72
-|[MSH2](MSH2)|2 |
73
-|[MSH6](MSH6)|2 |
74
-|[MYB](MYB)|2 |
75
-|[NCOR1](NCOR1)|2 |
76
-|[NF1](NF1)|2 |
77
-|[NFKB2](NFKB2)|2 |
78
-|[PHF6](PHF6)|2 |
79
-|[PIK3CD](PIK3CD)|2 |
80
-|[PTPN6](PTPN6)|2 |
81
-|[PTPRK](PTPRK)|2 |
82
-|[RARA](RARA)|2 |
83
-|[RUNX1](RUNX1)|2 |
84
-|[SETD1B](SETD1B)|1 |
85
-|[SETD5](SETD5)|2 |
86
-|[SYK](SYK)|2 |
87
-|[TGFBR2](TGFBR2)|2 |
88
-|[TIPARP](TIPARP)|2 |
89
-|[TOX](TOX)|1 |
90
-|[UBE2A](UBE2A)|1 |
91
-|[WAC](WAC)|2 |
92
-|[YY1](YY1)|2 |
93
-|[ZBTB7A](ZBTB7A)|2 |
94
-|[ZFAT](ZFAT)|2 |
95
-|[ZFX](ZFX)|2 |
96
-
97
-# Details
98
-
reichelFlowSortingExome2015a.md
... ...
@@ -1,67 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @reichelFlowSortingExome2015a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|11|18|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 11
26
-This study, PMBL Tier 2, 18
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[ARIH2](ARIH2)|2 |
37
-|[B2M](B2M)|1 |
38
-|[BCL7A](BCL7A)|2 |
39
-|[CSF2RB](CSF2RB)|1 |
40
-|[DMD](DMD)|2 |
41
-|[EBF1](EBF1)|1 |
42
-|[EEF1A1](EEF1A1)|1 |
43
-|[EGR1](EGR1)|2 |
44
-|[GNA13](GNA13)|1 |
45
-|[HECW2](HECW2)|2 |
46
-|[HELLS](HELLS)|2 |
47
-|[HIST1H1E](HIST1H1E)|1 |
48
-|[HIST1H3B](HIST1H3B)|2 |
49
-|[HIST1H4C](HIST1H4C)|2 |
50
-|[ITPKB](ITPKB)|1 |
51
-|[MPDZ](MPDZ)|2 |
52
-|[NEK1](NEK1)|2 |
53
-|[PIM2](PIM2)|1 |
54
-|[RANBP2](RANBP2)|2 |
55
-|[SENP7](SENP7)|2 |
56
-|[SETDB1](SETDB1)|2 |
57
-|[SIAH2](SIAH2)|2 |
58
-|[TBC1D15](TBC1D15)|2 |
59
-|[TICRR](TICRR)|2 |
60
-|[TRIP11](TRIP11)|2 |
61
-|[UBE2A](UBE2A)|1 |
62
-|[WEE1](WEE1)|1 |
63
-|[ZFP36L1](ZFP36L1)|1 |
64
-|[ZNF217](ZNF217)|2 |
65
-
66
-# Details
67
-
richterRecurrentMutationID32012a.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @richterRecurrentMutationID32012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|5||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1, 5
26
-This study, BL Tier 2,
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[CCND3](CCND3)|1 |
37
-|[FBXO11](FBXO11)|1 |
38
-|[ID3](ID3)|1 |
39
-|[RHOA](RHOA)|1 |
40
-|[SMARCA4](SMARCA4)|1 |
41
-
42
-# Details
43
-
ritzRecurrentMutationsSTAT62009a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @ritzRecurrentMutationsSTAT62009a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[STAT6](STAT6)|1 |
37
-
38
-# Details
39
-
rossiAlterationBIRC3Multiple2011a.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @rossiAlterationBIRC3Multiple2011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|4|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MZL Tier 1, 4
26
-This study, MZL Tier 2, 1
27
-Other MZL studies, MZL Tier 1, 42
28
-Other MZL studies, MZL Tier 2, 74
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MZL tier|
35
-|:-|:-:|
36
-|[BIRC3](BIRC3)|1 |
37
-|[IKBKB](IKBKB)|2 |
38
-|[MAP3K14](MAP3K14)|1 |
39
-|[TNFAIP3](TNFAIP3)|1 |
40
-|[TRAF3](TRAF3)|1 |
41
-
42
-# Details
43
-
rossiCodingGenomeSplenic2012c.md
... ...
@@ -1,60 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @rossiCodingGenomeSplenic2012c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|12|2|
12
-|MZL|10|11|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, MZL Tier 1, 10
27
-This study, MZL Tier 2, 11
28
-Other MZL studies, MZL Tier 1, 42
29
-Other MZL studies, MZL Tier 2, 74
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|DLBCL tier|MZL tier|
36
-|:-|:-:|:-:|
37
-|[ARID1A](ARID1A)|1 |1 |
38
-|[CD79A](CD79A)| |2 |
39
-|[DTX1](DTX1)|1 |1 |
40
-|[EGR1](EGR1)| |2 |
41
-|[EGR2](EGR2)| |2 |
42
-|[EP300](EP300)|1 |1 |
43
-|[GPS2](GPS2)| |2 |
44
-|[HIST1H2AG](HIST1H2AG)|2 |2 |
45
-|[HIST1H2BK](HIST1H2BK)|1 |2 |
46
-|[KMT2D](KMT2D)|1 |1 |
47
-|[MCRS1](MCRS1)| |2 |
48
-|[MSL2](MSL2)| |2 |
49
-|[NOTCH1](NOTCH1)|1 |1 |
50
-|[NOTCH2](NOTCH2)|1 |1 |
51
-|[SIN3A](SIN3A)|1 |1 |
52
-|[SPEN](SPEN)|1 |1 |
53
-|[SWAP70](SWAP70)| |2 |
54
-|[TBL1XR1](TBL1XR1)|1 |1 |
55
-|[TP53](TP53)|1 |1 |
56
-|[TRRAP](TRRAP)|1 |2 |
57
-|[WAC](WAC)|2 |2 |
58
-
59
-# Details
60
-
rushtonGeneticEvolutionaryPatterns2020.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @rushtonGeneticEvolutionaryPatterns2020
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[MS4A1](MS4A1)|1 |
37
-
38
-# Details
39
-
russler-germainMutationsAssociatedProgression2023b.md
... ...
@@ -1,58 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @russler-germainMutationsAssociatedProgression2023b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|19|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, FL Tier 1, 1
26
-This study, FL Tier 2, 19
27
-Other FL studies, FL Tier 1, 66
28
-Other FL studies, FL Tier 2, 50
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|FL tier|
35
-|:-|:-:|
36
-|[ABL2](ABL2)|2 |
37
-|[BCL10](BCL10)|2 |
38
-|[CD70](CD70)|2 |
39
-|[CD83](CD83)|1 |
40
-|[CILP](CILP)|2 |
41
-|[CYP2A6](CYP2A6)|2 |
42
-|[GBP7](GBP7)|2 |
43
-|[GRM6](GRM6)|2 |
44
-|[IGLL5](IGLL5)|2 |
45
-|[KIR3DL1](KIR3DL1)|2 |
46
-|[MAGEC1](MAGEC1)|2 |
47
-|[MAP7D1](MAP7D1)|2 |
48
-|[MKI67](MKI67)|2 |
49
-|[NFKBIA](NFKBIA)|2 |
50
-|[OR8H2](OR8H2)|2 |
51
-|[PZP](PZP)|2 |
52
-|[SHROOM3](SHROOM3)|2 |
53
-|[SRRM2](SRRM2)|2 |
54
-|[STAB2](STAB2)|2 |
55
-|[XIRP2](XIRP2)|2 |
56
-
57
-# Details
58
-
sarkozyMutationalLandscapeGray2021a.md
... ...
@@ -1,49 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @sarkozyMutationalLandscapeGray2021a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|5|6|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 5
26
-This study, PMBL Tier 2, 6
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[ABCA13](ABCA13)|2 |
37
-|[BCL2](BCL2)|2 |
38
-|[BIRC6](BIRC6)|1 |
39
-|[BTG1](BTG1)|1 |
40
-|[HIST1H1B](HIST1H1B)|1 |
41
-|[KMT2C](KMT2C)|1 |
42
-|[LRRN3](LRRN3)|2 |
43
-|[MFHAS1](MFHAS1)|2 |
44
-|[NCOR2](NCOR2)|2 |
45
-|[RELN](RELN)|2 |
46
-|[SPEN](SPEN)|1 |
47
-
48
-# Details
49
-
schmitzBurkittLymphomaPathogenesis2012.md
... ...
@@ -1,59 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schmitzBurkittLymphomaPathogenesis2012
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|4|16|
12
-|DLBCL|2|3|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, BL Tier 1, 4
27
-This study, BL Tier 2, 16
28
-Other BL studies, BL Tier 1, 29
29
-Other BL studies, BL Tier 2, 157
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|BL tier|DLBCL tier|
36
-|:-|:-:|:-:|
37
-|[C16orf48](C16orf48)|2 | |
38
-|[DDX3X](DDX3X)|1 |1 |
39
-|[DHCR7](DHCR7)|2 | |
40
-|[ELP2](ELP2)|2 | |
41
-|[EXOSC6](EXOSC6)|2 | |
42
-|[FLYWCH1](FLYWCH1)|2 | |
43
-|[FOXO1](FOXO1)|1 |1 |
44
-|[GTSE1](GTSE1)|2 | |
45
-|[ID3](ID3)|1 |2 |
46
-|[KANK2](KANK2)|2 | |
47
-|[MKI67](MKI67)|2 | |
48
-|[MYO18A](MYO18A)|2 | |
49
-|[NCOR2](NCOR2)|2 |2 |
50
-|[PCBP1](PCBP1)|2 |2 |
51
-|[PDCD11](PDCD11)|2 | |
52
-|[TCF3](TCF3)|1 | |
53
-|[TOP2A](TOP2A)|2 | |
54
-|[WDR90](WDR90)|2 | |
55
-|[WHAMM](WHAMM)|2 | |
56
-|[YY1AP1](YY1AP1)|2 | |
57
-
58
-# Details
59
-
schmitzGeneticsPathogenesisDiffuse2018a.md
... ...
@@ -1,54 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schmitzGeneticsPathogenesisDiffuse2018a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|7|9|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 7
26
-This study, DLBCL Tier 2, 9
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[CXCR5](CXCR5)|1 |
37
-|[DDX3X](DDX3X)|1 |
38
-|[DTX1](DTX1)|1 |
39
-|[FOXC1](FOXC1)|2 |
40
-|[GPC5](GPC5)|2 |
41
-|[GSG2](GSG2)|2 |
42
-|[HIST2H2BE](HIST2H2BE)|1 |
43
-|[ITPKB](ITPKB)|1 |
44
-|[KLHL21](KLHL21)|2 |
45
-|[LAMA5](LAMA5)|2 |
46
-|[MYBPC2](MYBPC2)|2 |
47
-|[NOL9](NOL9)|1 |
48
-|[PAPOLG](PAPOLG)|2 |
49
-|[PRKDC](PRKDC)|2 |
50
-|[TAP1](TAP1)|2 |
51
-|[WEE1](WEE1)|1 |
52
-
53
-# Details
54
-
schmitzTNFAIP3A20Tumor2009a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schmitzTNFAIP3A20Tumor2009a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[TNFAIP3](TNFAIP3)|1 |
37
-
38
-# Details
39
-
schneiderAlterationsCD58Gene2015a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schneiderAlterationsCD58Gene2015a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[CD58](CD58)|1 |
37
-
38
-# Details
39
-
schollMutationsRegionFAS2007.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @schollMutationsRegionFAS2007
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[FAS](FAS)|1 |
37
-
38
-# Details
39
-
shinBRAFV600EMAP2K12015.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @shinBRAFV600EMAP2K12015
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL||1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1,
26
-This study, DLBCL Tier 2, 1
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[MAP2K1](MAP2K1)|2 |
37
-
38
-# Details
39
-
spinaGeneticsNodalMarginal2016b.md
... ...
@@ -1,69 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @spinaGeneticsNodalMarginal2016b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|8|23|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MZL Tier 1, 8
26
-This study, MZL Tier 2, 23
27
-Other MZL studies, MZL Tier 1, 42
28
-Other MZL studies, MZL Tier 2, 74
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MZL tier|
35
-|:-|:-:|
36
-|[ABCA13](ABCA13)|2 |
37
-|[ACTG1](ACTG1)|2 |
38
-|[ADD2](ADD2)|2 |
39
-|[AMN](AMN)|2 |
40
-|[AOC2](AOC2)|2 |
41
-|[BCL10](BCL10)|1 |
42
-|[C6orf103](C6orf103)|2 |
43
-|[CDC42BPB](CDC42BPB)|2 |
44
-|[CDKN2A](CDKN2A)|2 |
45
-|[CLGN](CLGN)|2 |
46
-|[CNKSR2](CNKSR2)|2 |
47
-|[FAS](FAS)|1 |
48
-|[FAT1](FAT1)|1 |
49
-|[GPR98](GPR98)|2 |
50
-|[ID3](ID3)|1 |
51
-|[LRP1B](LRP1B)|2 |
52
-|[NCOR2](NCOR2)|1 |
53
-|[NOL9](NOL9)|1 |
54
-|[PACRG](PACRG)|2 |
55
-|[PARK2](PARK2)|2 |
56
-|[PLXNB3](PLXNB3)|2 |
57
-|[PTPRD](PTPRD)|1 |
58
-|[RCOR1](RCOR1)|2 |
59
-|[RPL1L](RPL1L)|2 |
60
-|[SAMD5](SAMD5)|2 |
61
-|[SCG3](SCG3)|2 |
62
-|[STXBP5](STXBP5)|2 |
63
-|[TAF1](TAF1)|2 |
64
-|[TCTN2](TCTN2)|2 |
65
-|[TNFRSF14](TNFRSF14)|1 |
66
-|[ZNF9](ZNF9)|2 |
67
-
68
-# Details
69
-
thomasGeneticSubgroupsInform2023.md
... ...
@@ -1,43 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @thomasGeneticSubgroupsInform2023
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|2|3|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1, 2
26
-This study, BL Tier 2, 3
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[CDKN2C](CDKN2C)|2 |
37
-|[EBF1](EBF1)|2 |
38
-|[EHD1](EHD1)|2 |
39
-|[PHF6](PHF6)|1 |
40
-|[WNK1](WNK1)|1 |
41
-
42
-# Details
43
-
tiacciBRAFMutationsHairycell2011a.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @tiacciBRAFMutationsHairycell2011a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[BRAF](BRAF)|1 |
37
-
38
-# Details
39
-
tiacciPervasiveMutationsJAKSTAT2018b.md
... ...
@@ -1,48 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @tiacciPervasiveMutationsJAKSTAT2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|9|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2, 9
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[AKAP6](AKAP6)|2 |
37
-|[DGKB](DGKB)|2 |
38
-|[ITPR3](ITPR3)|2 |
39
-|[NUP214](NUP214)|2 |
40
-|[PRUNE2](PRUNE2)|2 |
41
-|[SETD5](SETD5)|2 |
42
-|[STAT5B](STAT5B)|2 |
43
-|[TNIP1](TNIP1)|2 |
44
-|[TP53](TP53)|1 |
45
-|[ZCCHC11](ZCCHC11)|2 |
46
-
47
-# Details
48
-
troenNOTCH2MutationsMarginal2008.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @troenNOTCH2MutationsMarginal2008
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 1
26
-This study, DLBCL Tier 2,
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[NOTCH2](NOTCH2)|1 |
37
-
38
-# Details
39
-
vandenbrandRecurrentMutationsGenes2017.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @vandenbrandRecurrentMutationsGenes2017
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL||2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MZL Tier 1,
26
-This study, MZL Tier 2, 2
27
-Other MZL studies, MZL Tier 1, 42
28
-Other MZL studies, MZL Tier 2, 74
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MZL tier|
35
-|:-|:-:|
36
-|[CD9B](CD9B)|2 |
37
-|[TNIP2](TNIP2)|2 |
38
-
39
-# Details
40
-
viganoSomaticIL4RMutations2018b.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @viganoSomaticIL4RMutations2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2,
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[IL4R](IL4R)|1 |
37
-
38
-# Details
39
-
wenigerMutationsTumorSuppressor2006a.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @wenigerMutationsTumorSuppressor2006a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 1
26
-This study, PMBL Tier 2, 1
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[GPR126](GPR126)|2 |
37
-|[SOCS1](SOCS1)|1 |
38
-
39
-# Details
40
-
wienandGenomicAnalysesFlowsorted2019b.md
... ...
@@ -1,45 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @wienandGenomicAnalysesFlowsorted2019b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|4|3|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, PMBL Tier 1, 4
26
-This study, PMBL Tier 2, 3
27
-Other PMBL studies, PMBL Tier 1, 76
28
-Other PMBL studies, PMBL Tier 2, 82
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|PMBL tier|
35
-|:-|:-:|
36
-|[ACTB](ACTB)|1 |
37
-|[ARID1A](ARID1A)|1 |
38
-|[DNAH12](DNAH12)|2 |
39
-|[HLA-B](HLA-B)|1 |
40
-|[IKBKB](IKBKB)|2 |
41
-|[NFKBIA](NFKBIA)|1 |
42
-|[RBM38](RBM38)|2 |
43
-
44
-# Details
45
-
wildaInactivationARFMDM2p53Pathway2004.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @wildaInactivationARFMDM2p53Pathway2004
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1, 1
26
-This study, BL Tier 2,
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[TP53](TP53)|1 |
37
-
38
-# Details
39
-
wuGeneticHeterogeneityPrimary2016.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @wuGeneticHeterogeneityPrimary2016
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|1||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MCL Tier 1, 1
26
-This study, MCL Tier 2,
27
-Other MCL studies, MCL Tier 1, 23
28
-Other MCL studies, MCL Tier 2, 46
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MCL tier|
35
-|:-|:-:|
36
-|[CARD11](CARD11)|1 |
37
-
38
-# Details
39
-
yanBCRTLRSignaling2012a.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @yanBCRTLRSignaling2012a
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|2||
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MZL Tier 1, 2
26
-This study, MZL Tier 2,
27
-Other MZL studies, MZL Tier 1, 42
28
-Other MZL studies, MZL Tier 2, 74
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MZL tier|
35
-|:-|:-:|
36
-|[CARD11](CARD11)|1 |
37
-|[MYD88](MYD88)|1 |
38
-
39
-# Details
40
-
yildizActivatingSTAT6Mutations2015c.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @yildizActivatingSTAT6Mutations2015c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1||
12
-|DLBCL|1||
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 300
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, DLBCL Tier 1, 1
27
-This study, DLBCL Tier 2,
28
-Other DLBCL studies, DLBCL Tier 1, 128
29
-Other DLBCL studies, DLBCL Tier 2, 198
30
-```
31
-
32
-
33
-## Novel genes reported in this study
34
-
35
-|New gene|FL tier|DLBCL tier|
36
-|:-|:-:|:-:|
37
-|[STAT6](STAT6)|1 |1 |
38
-
39
-# Details
40
-
zhangGeneticHeterogeneityDiffuse2013.md
... ...
@@ -1,57 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @zhangGeneticHeterogeneityDiffuse2013
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|11|8|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, DLBCL Tier 1, 11
26
-This study, DLBCL Tier 2, 8
27
-Other DLBCL studies, DLBCL Tier 1, 128
28
-Other DLBCL studies, DLBCL Tier 2, 198
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[ARID1A](ARID1A)|1 |
37
-|[FBXW7](FBXW7)|1 |
38
-|[HIST1H3B](HIST1H3B)|1 |
39
-|[INO80](INO80)|2 |
40
-|[JAK1](JAK1)|2 |
41
-|[JAK3](JAK3)|2 |
42
-|[KLHL14](KLHL14)|1 |
43
-|[KMT2C](KMT2C)|1 |
44
-|[MGA](MGA)|1 |
45
-|[MTOR](MTOR)|1 |
46
-|[PIK3R1](PIK3R1)|2 |
47
-|[POU2F2](POU2F2)|1 |
48
-|[SETD2](SETD2)|2 |
49
-|[SMARCA4](SMARCA4)|1 |
50
-|[STAT5B](STAT5B)|2 |
51
-|[UBR5](UBR5)|2 |
52
-|[ZEB2](ZEB2)|2 |
53
-|[ZNF292](ZNF292)|1 |
54
-|[ZNF608](ZNF608)|1 |
55
-
56
-# Details
57
-
zhangGenomicLandscapeMantle2014.md
... ...
@@ -1,66 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @zhangGenomicLandscapeMantle2014
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|2|26|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, MCL Tier 1, 2
26
-This study, MCL Tier 2, 26
27
-Other MCL studies, MCL Tier 1, 23
28
-Other MCL studies, MCL Tier 2, 46
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|MCL tier|
35
-|:-|:-:|
36
-|[ANK2](ANK2)|2 |
37
-|[ATP11C](ATP11C)|2 |
38
-|[CDH8](CDH8)|2 |
39
-|[COL11A1](COL11A1)|2 |
40
-|[COL16A1](COL16A1)|2 |
41
-|[CTNNA2](CTNNA2)|2 |
42
-|[DHDH](DHDH)|2 |
43
-|[DLC1](DLC1)|2 |
44
-|[EIF2AK4](EIF2AK4)|2 |
45
-|[ESX1](ESX1)|2 |
46
-|[FAT4](FAT4)|2 |
47
-|[GRIN2A](GRIN2A)|2 |
48
-|[HEPH](HEPH)|2 |
49
-|[KMT2C](KMT2C)|2 |
50
-|[MRGPRF](MRGPRF)|2 |
51
-|[NIN](NIN)|2 |
52
-|[OGDHL](OGDHL)|2 |
53
-|[PCDHB2](PCDHB2)|2 |
54
-|[PLXNB3](PLXNB3)|2 |
55
-|[POT1](POT1)|1 |
56
-|[RB1](RB1)|1 |
57
-|[ROBO2](ROBO2)|2 |
58
-|[SALL3](SALL3)|2 |
59
-|[SI](SI)|2 |
60
-|[SMC1A](SMC1A)|2 |
61
-|[TBC1D26](TBC1D26)|2 |
62
-|[ZNF117](ZNF117)|2 |
63
-|[ZNF296](ZNF296)|2 |
64
-
65
-# Details
66
-
zhouSporadicEndemicBurkitt2019.md
... ...
@@ -1,39 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @zhouSporadicEndemicBurkitt2019
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL||1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 300
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, BL Tier 1,
26
-This study, BL Tier 2, 1
27
-Other BL studies, BL Tier 1, 29
28
-Other BL studies, BL Tier 2, 157
29
-```
30
-
31
-
32
-## Novel genes reported in this study
33
-
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[KMT2C](KMT2C)|2 |
37
-
38
-# Details
39
-