Changes in 4e3d59e: cleanup

				BCL6_tmp.html
			
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          -<p>[[<em>TOC</em>]]</p>

          -<h2 id="overview">Overview</h2>

          -<p>BCL6 is one of <a href="https://github.com/morinlab/LLMPP/wiki/ashm">a number of genes</a> affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.

          -Although common, particularly in DLBCL, the function of many of these mutations remains unclear but some have been shown to affect the regulation of BCL6 expression. The role of BCL6 missense mutations, seen over 9% of patients remains unclear.</p>

          -<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>

          -<p>[[include:table1_BCL6]]

          -|</p>

          -<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>

          -<p>[[include:DLBCL_BCL6.md]]

          -[[include:FL_BCL6.md]]

          -[[include:BL_BCL6.md]]</p>

          -<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>

          -<p>[[include:dnds_BCL6.md]]</p>

          -<h2 id="ashm-regions">aSHM regions</h2>

          -<table>

          -<thead>

          -<tr>

          -<th style="text-align:center">chr_name</th>

          -<th style="text-align:center">hg19_start</th>

          -<th style="text-align:center">hg19_end</th>

          -<th style="text-align:center">region</th>

          -<th style="text-align:center">regulatory_comment</th>

          -</tr>

          -</thead>

          -<tbody>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187458526</td>

          -<td style="text-align:center">187464632</td>

          -<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187458526%2D187464632">TSS</a></td>

          -<td style="text-align:center">NA</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187615533</td>

          -<td style="text-align:center">187625659</td>

          -<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187615533%2D187625659">Intergenic-1</a></td>

          -<td style="text-align:center">NA</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187625659</td>

          -<td style="text-align:center">187638101</td>

          -<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187625659%2D187638101">Intergenic-2</a></td>

          -<td style="text-align:center">NA</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187657518</td>

          -<td style="text-align:center">187665996</td>

          -<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187657518%2D187665996">Intergenic-3</a></td>

          -<td style="text-align:center">NA</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187675741</td>

          -<td style="text-align:center">187690717</td>

          -<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187675741%2D187690717">Intergenic-4</a></td>

          -<td style="text-align:center">NA</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187690717</td>

          -<td style="text-align:center">187705000</td>

          -<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187690717%2D187705000">Intergenic-5</a></td>

          -<td style="text-align:center">NA</td>

          -</tr>

          -</tbody>

          -</table>

          -<h2 id="bcl6-hotspots">BCL6 Hotspots</h2>

          -<table>

          -<thead>

          -<tr>

          -<th style="text-align:center">Chromosome</th>

          -<th style="text-align:center">Coordinate (hg19)</th>

          -<th style="text-align:center">ref&gt;alt</th>

          -<th style="text-align:center">HGVSp</th>

          -</tr>

          -</thead>

          -<tbody>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443373</td>

          -<td style="text-align:center">G&gt;A</td>

          -<td style="text-align:center">R585W</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443370</td>

          -<td style="text-align:center">G&gt;A</td>

          -<td style="text-align:center">P586S</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443369</td>

          -<td style="text-align:center">G&gt;A</td>

          -<td style="text-align:center">P586L</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443367</td>

          -<td style="text-align:center">C&gt;T</td>

          -<td style="text-align:center">A587T</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443366</td>

          -<td style="text-align:center">G&gt;T</td>

          -<td style="text-align:center">A587D</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443366</td>

          -<td style="text-align:center">G&gt;C</td>

          -<td style="text-align:center">A587G</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443345</td>

          -<td style="text-align:center">C&gt;T</td>

          -<td style="text-align:center">R594Q</td>

          -</tr>

          -<tr>

          -<td style="text-align:center">chr3</td>

          -<td style="text-align:center">187443342</td>

          -<td style="text-align:center">A&gt;T</td>

          -<td style="text-align:center">I595N</td>

          -</tr>

          -</tbody>

          -</table>

          -<p>[[include:browser_BCL6.md]]</p>

          -<h2 id="expression">Expression</h2>

          -<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BCL6_by_pathology.svg" alt=""></p>

          -<!-- ORIGIN: 21796119 -->

          -<!-- BL: loveGeneticLandscapeMutations2012 -->

          -<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

          -<h2 id="representative-mutations">Representative Mutations</h2>

          -<h3 id="bl">BL</h3>

          -<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Love_BCL6.svg" alt=""></p>

          -<p><strong>Rating</strong>

          -★ ★ ★ ★ ☆</p>

          -<h2 id="all-mutations">All Mutations</h2>

          -<h3 id="bl">BL</h3>

          -<p><a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/1090_reports.html">1090</a>

          -<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/747_reports.html">747</a></p>

          -<p>[[include:mermaid_BCL6.md]]</p>

          -<h2 id="references">References</h2>

          -

          -</body>

          -</html>

				DLBCL_sankey.md
			
          @@ -1,71 +0,0 @@

          -```mermaid

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          -Albuquerque 2017, DLBCL Tier 1, 3

          -Morin 2016, DLBCL Tier 1, 2

          -Schmitz 2018, DLBCL Tier 1, 7

          -Schmitz 2018, DLBCL Tier 2, 9

          -Pasqualucci 2001, DLBCL Tier 1, 2

          -Pasqualucci 2001, DLBCL Tier 2, 2

          -Pasqualucci 2011, DLBCL Tier 1, 3

          -Pasqualucci 2011, DLBCL Tier 2, 4

          -Chapuy 2018, DLBCL Tier 1, 2

          -Chapuy 2018, DLBCL Tier 2, 17

          -Zhang 2013, DLBCL Tier 1, 11

          -Zhang 2013, DLBCL Tier 2, 8

          -Pasqualucci 2011, DLBCL Tier 1, 2

          -Lohr 2012, DLBCL Tier 1, 3

          -Lohr 2012, DLBCL Tier 2, 1

          -Pararajalingam 2020, DLBCL Tier 2, 2

          -Hubschmann 2021, DLBCL Tier 1, 3

          -Hubschmann 2021, DLBCL Tier 2, 20

          -Mareschal 2016, DLBCL Tier 1, 2

          -Morin 2011, DLBCL Tier 1, 24

          -Morin 2011, DLBCL Tier 2, 1

          -Reddy 2017, DLBCL Tier 1, 7

          -Reddy 2017, DLBCL Tier 2, 53

          -Morin 2013, DLBCL Tier 1, 11

          -Morin 2013, DLBCL Tier 2, 29

          -Arthur 2018, DLBCL Tier 1, 8

          -Arthur 2018, DLBCL Tier 2, 12

          -DLBCL, exome, 2

          -exome, Mareschal 2016, 2

          -DLBCL, WGS, 23

          -WGS, Hubschmann 2021, 23

          -DLBCL, WGS/exome, 2

          -WGS/exome, Pararajalingam 2020, 2

          -DLBCL, exome, 4

          -exome, Lohr 2012, 4

          -DLBCL, exome, 19

          -exome, Zhang 2013, 19

          -DLBCL, exome, 2

          -exome, Pasqualucci 2011, 2

          -DLBCL, RNA-seq/WGS, 25

          -RNA-seq/WGS, Morin 2011, 25

          -DLBCL, exome, 60

          -exome, Reddy 2017, 60

          -DLBCL, WGS, 20

          -WGS, Arthur 2018, 20

          -DLBCL, WGS, 40

          -WGS, Morin 2013, 40

          -DLBCL, exome, 2

          -exome, Morin 2016, 2

          -DLBCL, exome, 3

          -exome, Albuquerque 2017, 3

          -DLBCL, exome, 16

          -exome, Schmitz 2018, 16

          -DLBCL, Sanger, 4

          -Sanger, Pasqualucci 2001, 4

          -DLBCL, exome, 7

          -exome, Pasqualucci 2011, 7

          -DLBCL, exome, 19

          -exome, Chapuy 2018, 19

          -```

				FL_genes.md
			
          @@ -9,7 +9,7 @@ nocite: |

           ## Origins of FL genes

          -![](FL_sankey-1.svg)

          +![](images/FL_sankey-1.svg)

           ## Tier 1 FL genes

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368		-<p>[[<em>TOC</em>]]</p>
369		-<h2 id="overview">Overview</h2>
370		-<p>BCL6 is one of <a href="https://github.com/morinlab/LLMPP/wiki/ashm">a number of genes</a> affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
371		-Although common, particularly in DLBCL, the function of many of these mutations remains unclear but some have been shown to affect the regulation of BCL6 expression. The role of BCL6 missense mutations, seen over 9% of patients remains unclear.</p>
372		-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
373		-<p>[[include:table1_BCL6]]
374		-\|</p>
375		-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
376		-<p>[[include:DLBCL_BCL6.md]]
377		-[[include:FL_BCL6.md]]
378		-[[include:BL_BCL6.md]]</p>
379		-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
380		-<p>[[include:dnds_BCL6.md]]</p>
381		-<h2 id="ashm-regions">aSHM regions</h2>
382		-<table>
383		-<thead>
384		-<tr>
385		-<th style="text-align:center">chr_name</th>
386		-<th style="text-align:center">hg19_start</th>
387		-<th style="text-align:center">hg19_end</th>
388		-<th style="text-align:center">region</th>
389		-<th style="text-align:center">regulatory_comment</th>
390		-</tr>
391		-</thead>
392		-<tbody>
393		-<tr>
394		-<td style="text-align:center">chr3</td>
395		-<td style="text-align:center">187458526</td>
396		-<td style="text-align:center">187464632</td>
397		-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187458526%2D187464632">TSS</a></td>
398		-<td style="text-align:center">NA</td>
399		-</tr>
400		-<tr>
401		-<td style="text-align:center">chr3</td>
402		-<td style="text-align:center">187615533</td>
403		-<td style="text-align:center">187625659</td>
404		-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187615533%2D187625659">Intergenic-1</a></td>
405		-<td style="text-align:center">NA</td>
406		-</tr>
407		-<tr>
408		-<td style="text-align:center">chr3</td>
409		-<td style="text-align:center">187625659</td>
410		-<td style="text-align:center">187638101</td>
411		-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187625659%2D187638101">Intergenic-2</a></td>
412		-<td style="text-align:center">NA</td>
413		-</tr>
414		-<tr>
415		-<td style="text-align:center">chr3</td>
416		-<td style="text-align:center">187657518</td>
417		-<td style="text-align:center">187665996</td>
418		-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187657518%2D187665996">Intergenic-3</a></td>
419		-<td style="text-align:center">NA</td>
420		-</tr>
421		-<tr>
422		-<td style="text-align:center">chr3</td>
423		-<td style="text-align:center">187675741</td>
424		-<td style="text-align:center">187690717</td>
425		-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187675741%2D187690717">Intergenic-4</a></td>
426		-<td style="text-align:center">NA</td>
427		-</tr>
428		-<tr>
429		-<td style="text-align:center">chr3</td>
430		-<td style="text-align:center">187690717</td>
431		-<td style="text-align:center">187705000</td>
432		-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187690717%2D187705000">Intergenic-5</a></td>
433		-<td style="text-align:center">NA</td>
434		-</tr>
435		-</tbody>
436		-</table>
437		-<h2 id="bcl6-hotspots">BCL6 Hotspots</h2>
438		-<table>
439		-<thead>
440		-<tr>
441		-<th style="text-align:center">Chromosome</th>
442		-<th style="text-align:center">Coordinate (hg19)</th>
443		-<th style="text-align:center">ref>alt</th>
444		-<th style="text-align:center">HGVSp</th>
445		-</tr>
446		-</thead>
447		-<tbody>
448		-<tr>
449		-<td style="text-align:center">chr3</td>
450		-<td style="text-align:center">187443373</td>
451		-<td style="text-align:center">G>A</td>
452		-<td style="text-align:center">R585W</td>
453		-</tr>
454		-<tr>
455		-<td style="text-align:center">chr3</td>
456		-<td style="text-align:center">187443370</td>
457		-<td style="text-align:center">G>A</td>
458		-<td style="text-align:center">P586S</td>
459		-</tr>
460		-<tr>
461		-<td style="text-align:center">chr3</td>
462		-<td style="text-align:center">187443369</td>
463		-<td style="text-align:center">G>A</td>
464		-<td style="text-align:center">P586L</td>
465		-</tr>
466		-<tr>
467		-<td style="text-align:center">chr3</td>
468		-<td style="text-align:center">187443367</td>
469		-<td style="text-align:center">C>T</td>
470		-<td style="text-align:center">A587T</td>
471		-</tr>
472		-<tr>
473		-<td style="text-align:center">chr3</td>
474		-<td style="text-align:center">187443366</td>
475		-<td style="text-align:center">G>T</td>
476		-<td style="text-align:center">A587D</td>
477		-</tr>
478		-<tr>
479		-<td style="text-align:center">chr3</td>
480		-<td style="text-align:center">187443366</td>
481		-<td style="text-align:center">G>C</td>
482		-<td style="text-align:center">A587G</td>
483		-</tr>
484		-<tr>
485		-<td style="text-align:center">chr3</td>
486		-<td style="text-align:center">187443345</td>
487		-<td style="text-align:center">C>T</td>
488		-<td style="text-align:center">R594Q</td>
489		-</tr>
490		-<tr>
491		-<td style="text-align:center">chr3</td>
492		-<td style="text-align:center">187443342</td>
493		-<td style="text-align:center">A>T</td>
494		-<td style="text-align:center">I595N</td>
495		-</tr>
496		-</tbody>
497		-</table>
498		-<p>[[include:browser_BCL6.md]]</p>
499		-<h2 id="expression">Expression</h2>
500		-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BCL6_by_pathology.svg" alt=""></p>
501		-<!-- ORIGIN: 21796119 -->
502		-<!-- BL: loveGeneticLandscapeMutations2012 -->
503		-<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
504		-<h2 id="representative-mutations">Representative Mutations</h2>
505		-<h3 id="bl">BL</h3>
506		-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Love_BCL6.svg" alt=""></p>
507		-<p><strong>Rating</strong>
508		-★ ★ ★ ★ ☆</p>
509		-<h2 id="all-mutations">All Mutations</h2>
510		-<h3 id="bl">BL</h3>
511		-<p><a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/1090_reports.html">1090</a>
512		-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/747_reports.html">747</a></p>
513		-<p>[[include:mermaid_BCL6.md]]</p>
514		-<h2 id="references">References</h2>
515		-
516		-</body>
517		-</html>

...	...	@@ -1,71 +0,0 @@
1		-```mermaid
2		----
3		-config:
4		- sankey:
5		- showValues: false
6		- linkColor: target
7		- width: 800
8		- height: 1000
9		- nodeAlignment: right
10		----
11		-sankey-beta
12		-Albuquerque 2017, DLBCL Tier 1, 3
13		-Morin 2016, DLBCL Tier 1, 2
14		-Schmitz 2018, DLBCL Tier 1, 7
15		-Schmitz 2018, DLBCL Tier 2, 9
16		-Pasqualucci 2001, DLBCL Tier 1, 2
17		-Pasqualucci 2001, DLBCL Tier 2, 2
18		-Pasqualucci 2011, DLBCL Tier 1, 3
19		-Pasqualucci 2011, DLBCL Tier 2, 4
20		-Chapuy 2018, DLBCL Tier 1, 2
21		-Chapuy 2018, DLBCL Tier 2, 17
22		-Zhang 2013, DLBCL Tier 1, 11
23		-Zhang 2013, DLBCL Tier 2, 8
24		-Pasqualucci 2011, DLBCL Tier 1, 2
25		-Lohr 2012, DLBCL Tier 1, 3
26		-Lohr 2012, DLBCL Tier 2, 1
27		-Pararajalingam 2020, DLBCL Tier 2, 2
28		-Hubschmann 2021, DLBCL Tier 1, 3
29		-Hubschmann 2021, DLBCL Tier 2, 20
30		-Mareschal 2016, DLBCL Tier 1, 2
31		-Morin 2011, DLBCL Tier 1, 24
32		-Morin 2011, DLBCL Tier 2, 1
33		-Reddy 2017, DLBCL Tier 1, 7
34		-Reddy 2017, DLBCL Tier 2, 53
35		-Morin 2013, DLBCL Tier 1, 11
36		-Morin 2013, DLBCL Tier 2, 29
37		-Arthur 2018, DLBCL Tier 1, 8
38		-Arthur 2018, DLBCL Tier 2, 12
39		-DLBCL, exome, 2
40		-exome, Mareschal 2016, 2
41		-DLBCL, WGS, 23
42		-WGS, Hubschmann 2021, 23
43		-DLBCL, WGS/exome, 2
44		-WGS/exome, Pararajalingam 2020, 2
45		-DLBCL, exome, 4
46		-exome, Lohr 2012, 4
47		-DLBCL, exome, 19
48		-exome, Zhang 2013, 19
49		-DLBCL, exome, 2
50		-exome, Pasqualucci 2011, 2
51		-DLBCL, RNA-seq/WGS, 25
52		-RNA-seq/WGS, Morin 2011, 25
53		-DLBCL, exome, 60
54		-exome, Reddy 2017, 60
55		-DLBCL, WGS, 20
56		-WGS, Arthur 2018, 20
57		-DLBCL, WGS, 40
58		-WGS, Morin 2013, 40
59		-DLBCL, exome, 2
60		-exome, Morin 2016, 2
61		-DLBCL, exome, 3
62		-exome, Albuquerque 2017, 3
63		-DLBCL, exome, 16
64		-exome, Schmitz 2018, 16
65		-DLBCL, Sanger, 4
66		-Sanger, Pasqualucci 2001, 4
67		-DLBCL, exome, 7
68		-exome, Pasqualucci 2011, 7
69		-DLBCL, exome, 19
70		-exome, Chapuy 2018, 19
71		-```

...	...	@@ -9,7 +9,7 @@ nocite: \|
9	9
10	10	## Origins of FL genes
11	11
12		-![](FL_sankey-1.svg)
	12	+![](images/FL_sankey-1.svg)
13	13
14	14
15	15	## Tier 1 FL genes