ABI3BP.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
37 37
![image](images/proteinpaint/ABI3BP.svg)
38 38
## ABI3BP Expression
39 39
![image](images/gene_expression/ABI3BP_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
ACTB.md
... ...
@@ -35,9 +35,6 @@ ACTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
35 35
|:--------:|:----------:|:--------:|:---------------------------------------------------------------------------------------:|:------------------:|
36 36
|chr7 |5568297 |5570856 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr7%3A5568297%2D5570856)|active_promoter |
37 37
38
-> [!NOTE]
39
-> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
40
-
41 38
## ACTB Hotspots
42 39
43 40
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -61,5 +58,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
61 58
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ACTB.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ACTB_hg38.html)
62 59
63 60
![image](images/proteinpaint/ACTB.svg)
61
+
62
+
64 63
## ACTB Expression
65 64
![image](images/gene_expression/ACTB_by_pathology.svg)
65
+
66
+## References
67
+1. *Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.*
68
+
69
+<!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->
ACTG1.md
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
44 44
![image](images/proteinpaint/ACTG1.svg)
45 45
## ACTG1 Expression
46 46
![image](images/gene_expression/ACTG1_by_pathology.svg)
47
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
ADAMTS1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
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![image](images/proteinpaint/ADAMTS1.svg)
38 38
## ADAMTS1 Expression
39 39
![image](images/gene_expression/ADAMTS1_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
AICDA.md
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
42 42
![image](images/proteinpaint/AICDA.svg)
43 43
## AICDA Expression
44 44
![image](images/gene_expression/AICDA_by_pathology.svg)
45
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
ANKRD12.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
37 37
![image](images/proteinpaint/ANKRD12.svg)
38 38
## ANKRD12 Expression
39 39
![image](images/gene_expression/ANKRD12_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
ANKRD17.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
37 37
![image](images/proteinpaint/ANKRD17.svg)
38 38
## ANKRD17 Expression
39 39
![image](images/gene_expression/ANKRD17_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ARID1A.md
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
45 45
![image](images/proteinpaint/ARID1A.svg)
46 46
## ARID1A Expression
47 47
![image](images/gene_expression/ARID1A_by_pathology.svg)
48
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
ARID1B.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
39 39
![image](images/proteinpaint/ARID1B.svg)
40 40
## ARID1B Expression
41 41
![image](images/gene_expression/ARID1B_by_pathology.svg)
42
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ARID5B.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
39 39
![image](images/proteinpaint/ARID5B.svg)
40 40
## ARID5B Expression
41 41
![image](images/gene_expression/ARID5B_by_pathology.svg)
42
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ATM.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
39 39
![image](images/proteinpaint/ATM.svg)
40 40
## ATM Expression
41 41
![image](images/gene_expression/ATM_by_pathology.svg)
42
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ATR.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
37 37
![image](images/proteinpaint/ATR.svg)
38 38
## ATR Expression
39 39
![image](images/gene_expression/ATR_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
Audit-of-B\342\200\220cell-Cancer-Genes.md
... ...
@@ -1,3 +1,4 @@
1 1
2 2
This is a community-driven resource and knowledge base initiated by members of the Lymphoma/Leukemia Molecular Profiling Project and fuelled by results from the genomic analysis of mature B-cell lymphomas (GAMBL) project. ## ATR Expression
3 3
![image](images/gene_expression/ATR_by_pathology.svg)
4
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
B2M.md
... ...
@@ -78,4 +78,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
78 78
79 79
80 80
## References
81
-1. *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.*
... ...
\ No newline at end of file
0
+1. *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.*<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
BCL10.md
... ...
@@ -57,3 +57,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
57 57
58 58
2. *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.*## BCL10 Expression
59 59
![image](images/gene_expression/BCL10_by_pathology.svg)
60
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
BCL6.md
... ...
@@ -76,3 +76,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
76 76
3. *Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407. doi: 10.1056/NEJMoa1801445. PMID: 29641966; PMCID: PMC6010183.*
77 77
## BCL6 Expression
78 78
![image](images/gene_expression/BCL6_by_pathology.svg)
79
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
BCL7A.md
... ...
@@ -56,3 +56,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
56 56
3. *Baliñas-Gavira C, Rodríguez MI, Andrades A, Cuadros M, Álvarez-Pérez JC, Álvarez-Prado ÁF, de Yébenes VG, Sánchez-Hernández S, Fernández-Vigo E, Muñoz J, Martín F, Ramiro AR, Martínez-Climent JA, Medina PP. Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL. Leukemia. 2020 Oct;34(10):2722-2735. doi: 10.1038/s41375-020-0919-5. Epub 2020 Jun 24. PMID: 32576963.*
57 57
## BCL7A Expression
58 58
![image](images/gene_expression/BCL7A_by_pathology.svg)
59
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
BIRC3.md
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
44 44
![image](images/proteinpaint/BIRC3.svg)
45 45
## BIRC3 Expression
46 46
![image](images/gene_expression/BIRC3_by_pathology.svg)
47
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
BIRC6.md
... ...
@@ -56,3 +56,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
56 56
1. *Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765-1776. doi: 10.1182/blood.2020007507. PMID: 32961552.*
57 57
## BIRC6 Expression
58 58
![image](images/gene_expression/BIRC6_by_pathology.svg)
59
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
BRAF.md
... ...
@@ -58,7 +58,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
58 58
59 59
![image](images/proteinpaint/BRAF.svg)
60 60
61
-## References
62
-1. *Kamata T, Hussain J, Giblett S, Hayward R, Marais R, Pritchard C. BRAF inactivation drives aneuploidy by deregulating CRAF. Cancer Res. 2010 Nov 1;70(21):8475-86. doi: 10.1158/0008-5472.CAN-10-0603. Epub 2010 Oct 26. PMID: 20978199; PMCID: PMC2975377.*
63 61
## BRAF Expression
64 62
![image](images/gene_expression/BRAF_by_pathology.svg)
63
+
64
+## References
65
+1. *Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foà R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R, Falini B. BRAF mutations in hairy-cell leukemia. N Engl J Med. 2011 Jun 16;364(24):2305-15. doi: 10.1056/NEJMoa1014209. Epub 2011 Jun 11. PMID: 21663470; PMCID: PMC3689585.*
66
+2. *Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.*
67
+
68
+<!-- ORIGIN: tiacciBRAFMutationsHairycell2011a -->
BRINP3.md
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
40 40
![image](images/proteinpaint/BRINP3.svg)
41 41
## BRINP3 Expression
42 42
![image](images/gene_expression/BRINP3_by_pathology.svg)
43
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
BTBD3.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
37 37
![image](images/proteinpaint/BTBD3.svg)
38 38
## BTBD3 Expression
39 39
![image](images/gene_expression/BTBD3_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
BTG1.md
... ...
@@ -83,3 +83,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
83 83
3. *Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science. 2023 Jan 20;379(6629):eabj7412. doi: 10.1126/science.abj7412. Epub 2023 Jan 20. PMID: 36656933; PMCID: PMC10515739.*
84 84
4. *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.*## BTG1 Expression
85 85
![image](images/gene_expression/BTG1_by_pathology.svg)
86
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
BTG2.md
... ...
@@ -54,3 +54,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
54 54
2. *Guo D, Hong L, Ji H, Jiang Y, Lu L, Wang X, Huang H. The Mutation of BTG2 Gene Predicts a Poor Outcome in Primary Testicular Diffuse Large B-Cell Lymphoma. J Inflamm Res. 2022 Mar 10;15:1757-1769. doi: 10.2147/JIR.S341355. PMID: 35300216; PMCID: PMC8923029.*
55 55
3. *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.*## BTG2 Expression
56 56
![image](images/gene_expression/BTG2_by_pathology.svg)
57
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
BTK.md
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
41 41
2. *Schejbel L, Breinholt MF, Gang AO, Nielsen TH, Pedersen LM, Høgdall E, Nørgaard P. Inactivating BTK mutations in large B-cell lymphoma in a real-world cohort: Strong correlation with BCL2 translocation. EJHaem. 2022 Jun 24;3(3):936-939. doi: 10.1002/jha2.489. PMID: 36051027; PMCID: PMC9421985.*
42 42
## BTK Expression
43 43
![image](images/gene_expression/BTK_by_pathology.svg)
44
+<!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a -->
CADPS2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
![image](images/proteinpaint/CADPS2.svg)
38 38
## CADPS2 Expression
39 39
![image](images/gene_expression/CADPS2_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
CARD11.md
... ...
@@ -67,3 +67,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
67 67
1. *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.*
68 68
## CARD11 Expression
69 69
![image](images/gene_expression/CARD11_by_pathology.svg)
70
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
CASP8.md
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@@ -46,3 +46,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
46 46
2. *Hakem A, El Ghamrasni S, Maire G, Lemmers B, Karaskova J, Jurisicova A, Sanchez O, Squire J, Hakem R. Caspase-8 is essential for maintaining chromosomal stability and suppressing B-cell lymphomagenesis. Blood. 2012 Apr 12;119(15):3495-502. doi: 10.1182/blood-2011-07-367532. Epub 2012 Feb 16. PMID: 22343728.*
47 47
## CASP8 Expression
48 48
![image](images/gene_expression/CASP8_by_pathology.svg)
49
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
CBLB.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
![image](images/proteinpaint/CBLB.svg)
38 38
## CBLB Expression
39 39
![image](images/gene_expression/CBLB_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
CCL4.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
![image](images/proteinpaint/CCL4.svg)
38 38
## CCL4 Expression
39 39
![image](images/gene_expression/CCL4_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
CCND3.md
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@@ -90,3 +90,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
90 90
2. *Schmitz, R., et al. (2012). "Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics." Nature, 490(7418), 116-120.*
91 91
## CCND3 Expression
92 92
![image](images/gene_expression/CCND3_by_pathology.svg)
93
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
CD22.md
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37 37
![image](images/proteinpaint/CD22.svg)
38 38
## CD22 Expression
39 39
![image](images/gene_expression/CD22_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
CD274.md
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@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
43 43
1. *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.*
44 44
2. *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.*## CD274 Expression
45 45
![image](images/gene_expression/CD274_by_pathology.svg)
46
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
CD36.md
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43 43
1. *Carreras J, Ikoma H, Kikuti YY, Miyaoka M, Hiraiwa S, Tomita S, Kondo Y, Ito A, Nagase S, Miura H, Kawada H, Roncador G, Campo E, Hamoudi R, Nakamura N. Mutational, immune microenvironment, and clinicopathological profiles of diffuse large B-cell lymphoma and follicular lymphoma with BCL6 rearrangement. Virchows Arch. 2024 Apr;484(4):657-676. doi: 10.1007/s00428-024-03774-z. Epub 2024 Mar 11. PMID: 38462571.*
44 44
## CD36 Expression
45 45
![image](images/gene_expression/CD36_by_pathology.svg)
46
+<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
CD44.md
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@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
42 42
![image](images/proteinpaint/CD44.svg)
43 43
## CD44 Expression
44 44
![image](images/gene_expression/CD44_by_pathology.svg)
45
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
CD58.md
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@@ -48,3 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
48 48
1. *Challa-Malladi M, Lieu YK, Califano O, Holmes AB, Bhagat G, Murty VV, Dominguez-Sola D, Pasqualucci L, Dalla-Favera R. Combined genetic inactivation of β2-Microglobulin and CD58 reveals frequent escape from immune recognition in diffuse large B cell lymphoma. Cancer Cell. 2011 Dec 13;20(6):728-40. doi: 10.1016/j.ccr.2011.11.006. Epub 2011 Dec 1. PMID: 22137796; PMCID: PMC3660995.*
49 49
2. *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.*## CD58 Expression
50 50
![image](images/gene_expression/CD58_by_pathology.svg)
51
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
CD70.md
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56 56
3. *Mandato, E., Calabretta, E., Bai, G., Song, L., Sun, Y., Shanmugam, V., Paczkowska, J., Choi, I., Redd, R., Tang, M., Lawton, L., Neuberg, D., Rodig, S., Michor, F., Zhang, B., & Shipp, M. (2022). Abstract A38: Cd70 genetic perturbation limits the development of an effective CD8+ T-cell immune response to Bcl6-driven diffuse large B-cell lymphoma. Blood Cancer Discovery. https://doi.org/10.1158/2643-3249.lymphoma22-a38.*
57 57
## CD70 Expression
58 58
![image](images/gene_expression/CD70_by_pathology.svg)
59
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
CD74.md
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42 42
![image](images/proteinpaint/CD74.svg)
43 43
## CD74 Expression
44 44
![image](images/gene_expression/CD74_by_pathology.svg)
45
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
CD79B.md
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69 69
3. *Wilson WH, Wright GW, Huang DW, Hodkinson B, Balasubramanian S, Fan Y, Vermeulen J, Shreeve M, Staudt LM. Effect of ibrutinib with R-CHOP chemotherapy in genetic subtypes of DLBCL. Cancer Cell. 2021 Dec 13;39(12):1643-1653.e3. doi: 10.1016/j.ccell.2021.10.006. Epub 2021 Nov 4. PMID: 34739844; PMCID: PMC8722194.*
70 70
4. *Kim Y, Ju H, Kim DH, Yoo HY, Kim SJ, Kim WS, Ko YH. CD79B and MYD88 mutations in diffuse large B-cell lymphoma. Hum Pathol. 2014 Mar;45(3):556-64. doi: 10.1016/j.humpath.2013.10.023. Epub 2013 Oct 31. PMID: 24444466.*## CD79B Expression
71 71
![image](images/gene_expression/CD79B_by_pathology.svg)
72
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
CD83.md
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@@ -55,3 +55,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
55 55
2. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PMID: 23699601; PMCID: PMC3744992.*
56 56
3. *Russler-Germain DA, Krysiak K, Ramirez C, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen AF, Mehta-Shah N, Kahl BS, Bartlett NL, Alderuccio JP, Lossos IS, Ondrejka SL, Hsi ED, Martin P, Leonard JP, Griffith M, Griffith OL, Fehniger TA. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Adv. 2023 Sep 26;7(18):5524-5539. doi: 10.1182/bloodadvances.2023010779. PMID: 37493986; PMCID: PMC10514406.*## CD83 Expression
57 57
![image](images/gene_expression/CD83_by_pathology.svg)
58
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
CDC73.md
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@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
41 41
![image](images/proteinpaint/CDC73.svg)
42 42
## CDC73 Expression
43 43
![image](images/gene_expression/CDC73_by_pathology.svg)
44
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
CDH9.md
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37 37
![image](images/proteinpaint/CDH9.svg)
38 38
## CDH9 Expression
39 39
![image](images/gene_expression/CDH9_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
CDKN2A.md
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53 53
## References
54 54
1. *Guney S, Jardin F, Bertrand P, Mareschal S, Parmentier F, Picquenot JM, Tilly H, Bastard C. Several mechanisms lead to the inactivation of the CDKN2A (P16), P14ARF, or CDKN2B (P15) genes in the GCB and ABC molecular DLBCL subtypes. Genes Chromosomes Cancer. 2012 Sep;51(9):858-67. doi: 10.1002/gcc.21970. Epub 2012 May 23. PMID: 22619049.*## CDKN2A Expression
55 55
![image](images/gene_expression/CDKN2A_by_pathology.svg)
56
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
CHD1.md
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37 37
![image](images/proteinpaint/CHD1.svg)
38 38
## CHD1 Expression
39 39
![image](images/gene_expression/CHD1_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
CHD8.md
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41 41
![image](images/proteinpaint/CHD8.svg)
42 42
## CHD8 Expression
43 43
![image](images/gene_expression/CHD8_by_pathology.svg)
44
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
CHST2.md
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37 37
![image](images/proteinpaint/CHST2.svg)
38 38
## CHST2 Expression
39 39
![image](images/gene_expression/CHST2_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
CIITA.md
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48 48
2. *Sarah T Wilkinson, Diane R Fernandez, Shawn P Murphy, Wing C. Chan, Randy D. Gascoyne, Elias Campo, Elaine S. Jaffe, Louis M. Staudt, Jan Delabie, Andreas Rosenwald, Lisa M Rimsza; Loss of CIITA and MHC Class II Expression in Diffuse Large B-Cell Lymphoma Is Not Explained by Methylation of CIITA Promoters III and IV.. Blood 2008; 112 (11): 1786. doi: https://doi.org/10.1182/blood.V112.11.1786.1786*
49 49
3. *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.*## CIITA Expression
50 50
![image](images/gene_expression/CIITA_by_pathology.svg)
51
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
CNOT2.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37 37
![image](images/proteinpaint/CNOT2.svg)
38 38
## CNOT2 Expression
39 39
![image](images/gene_expression/CNOT2_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
CNTNAP5.md
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37 37
![image](images/proteinpaint/CNTNAP5.svg)
38 38
## CNTNAP5 Expression
39 39
![image](images/gene_expression/CNTNAP5_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
COQ7.md
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37 37
![image](images/proteinpaint/COQ7.svg)
38 38
## COQ7 Expression
39 39
![image](images/gene_expression/COQ7_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
CREBBP.md
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79 79
2. *Dreval K, Hilton LK, Cruz M, Shaalan H, Ben-Neriah S, Boyle M, Collinge B, Coyle KM, Duns G, Farinha P, Grande BM, Meissner B, Pararajalingam P, Rushton CK, Slack GW, Wong J, Mungall AJ, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns. Blood. 2023 Aug 10;142(6):561-573. doi: 10.1182/blood.2022018719. PMID: 37084389; PMCID: PMC10644066.*
80 80
## CREBBP Expression
81 81
![image](images/gene_expression/CREBBP_by_pathology.svg)
82
+<!-- ORIGIN: pasqualucciInactivatingMutationsAcetyltransferase2011a -->
CRIP1.md
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37 37
![image](images/proteinpaint/CRIP1.svg)
38 38
## CRIP1 Expression
39 39
![image](images/gene_expression/CRIP1_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
CXCR4.md
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@@ -52,3 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
52 52
![image](images/proteinpaint/CXCR4.svg)
53 53
## CXCR4 Expression
54 54
![image](images/gene_expression/CXCR4_by_pathology.svg)
55
+<!-- ORIGIN: khodabakhshiRecurrentTargetsAberrant2012 -->
CXCR5.md
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44 44
![image](images/proteinpaint/CXCR5.svg)
45 45
## CXCR5 Expression
46 46
![image](images/gene_expression/CXCR5_by_pathology.svg)
47
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
DAZAP1.md
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53 53
## References
54 54
1. *Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572-584. doi: 10.1182/blood.2019002385. PMID: 32160292; PMCID: PMC7440974.*## DAZAP1 Expression
55 55
![image](images/gene_expression/DAZAP1_by_pathology.svg)
56
+<!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 -->
DCAF6.md
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37 37
![image](images/proteinpaint/DCAF6.svg)
38 38
## DCAF6 Expression
39 39
![image](images/gene_expression/DCAF6_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
DDX10.md
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37 37
![image](images/proteinpaint/DDX10.svg)
38 38
## DDX10 Expression
39 39
![image](images/gene_expression/DDX10_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
DDX3X.md
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56 56
57 57
## DDX3X Expression
58 58
![image](images/gene_expression/DDX3X_by_pathology.svg)
59
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
DHX16.md
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37 37
![image](images/proteinpaint/DHX16.svg)
38 38
## DHX16 Expression
39 39
![image](images/gene_expression/DHX16_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
DICER1.md
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40 40
![image](images/proteinpaint/DICER1.svg)
41 41
## DICER1 Expression
42 42
![image](images/gene_expression/DICER1_by_pathology.svg)
43
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
DNAH5.md
... ...
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37 37
![image](images/proteinpaint/DNAH5.svg)
38 38
## DNAH5 Expression
39 39
![image](images/gene_expression/DNAH5_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
DNM2.md
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43 43
![image](images/proteinpaint/DNM2.svg)
44 44
## DNM2 Expression
45 45
![image](images/gene_expression/DNM2_by_pathology.svg)
46
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
DNMT3A.md
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37 37
![image](images/proteinpaint/DNMT3A.svg)
38 38
## DNMT3A Expression
39 39
![image](images/gene_expression/DNMT3A_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
DOCK1.md
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37 37
![image](images/proteinpaint/DOCK1.svg)
38 38
## DOCK1 Expression
39 39
![image](images/gene_expression/DOCK1_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
DSG4.md
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37 37
![image](images/proteinpaint/DSG4.svg)
38 38
## DSG4 Expression
39 39
![image](images/gene_expression/DSG4_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
DTX1.md
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101 101
1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.*
102 102
2. *de Miranda NF, Georgiou K, Chen L, Wu C, Gao Z, Zaravinos A, Lisboa S, Enblad G, Teixeira MR, Zeng Y, Peng R, Pan-Hammarström Q. Exome sequencing reveals novel mutation targets in diffuse large B-cell lymphomas derived from Chinese patients. Blood. 2014 Oct 16;124(16):2544-53. doi: 10.1182/blood-2013-12-546309. Epub 2014 Aug 29. PMID: 25171927; PMCID: PMC4199956.*## DTX1 Expression
103 103
![image](images/gene_expression/DTX1_by_pathology.svg)
104
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
DUSP2.md
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67 67
3. *Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407. doi: 10.1056/NEJMoa1801445. PMID: 29641966; PMCID: PMC6010183.*
68 68
## DUSP2 Expression
69 69
![image](images/gene_expression/DUSP2_by_pathology.svg)
70
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
EBF1.md
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69 69
1. *Györy I, Boller S, Nechanitzky R, Mandel E, Pott S, Liu E, Grosschedl R. Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells. Genes Dev. 2012 Apr 1;26(7):668-82. doi: 10.1101/gad.187328.112. Epub 2012 Mar 19. PMID: 22431510; PMCID: PMC3323878.*
70 70
## EBF1 Expression
71 71
![image](images/gene_expression/EBF1_by_pathology.svg)
72
+<!-- ORIGIN: bohleRoleEarlyBcell2013 -->
EEF1A1.md
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55 55
2. *Gong T, Shuang Y. Expression and Clinical Value of Eukaryotic Translation Elongation Factor 1A1 (EEF1A1) in Diffuse Large B Cell Lymphoma. Int J Gen Med. 2021 Oct 27;14:7247-7258. doi: 10.2147/IJGM.S324645. PMID: 34737619; PMCID: PMC8559353.*
56 56
## EEF1A1 Expression
57 57
![image](images/gene_expression/EEF1A1_by_pathology.svg)
58
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
EP300.md
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81 81
82 82
4. *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.*## EP300 Expression
83 83
![image](images/gene_expression/EP300_by_pathology.svg)
84
+<!-- ORIGIN: pasqualucciInactivatingMutationsAcetyltransferase2011a -->
ETS1.md
... ...
@@ -75,3 +75,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
75 75
## References
76 76
1. *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.*## ETS1 Expression
77 77
![image](images/gene_expression/ETS1_by_pathology.svg)
78
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
ETV6.md
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
50 50
![image](images/proteinpaint/ETV6.svg)
51 51
## ETV6 Expression
52 52
![image](images/gene_expression/ETV6_by_pathology.svg)
53
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
EZH2.md
... ...
@@ -67,3 +67,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
67 67
3. *Morin RD, Arthur SE, Assouline S. Treating lymphoma is now a bit EZ-er. Blood Adv. 2021 Apr 27;5(8):2256-2263. doi: 10.1182/bloodadvances.2020002773. PMID: 33904892; PMCID: PMC8095133.*
68 68
4. *Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904-916. doi: 10.1182/blood.2022016534. PMID: 36201743; PMCID: PMC10023728.*## EZH2 Expression
69 69
![image](images/gene_expression/EZH2_by_pathology.svg)
70
+<!-- ORIGIN: morinSomaticMutationsAltering2010 -->
FAM38B.md
... ...
@@ -24,3 +24,4 @@
24 24
> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
25 25
## FAM38B Expression
26 26
![image](images/gene_expression/FAM38B_by_pathology.svg)
27
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
FAS.md
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@@ -49,3 +49,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
49 49
5. *Rys, R., Venkataraman, M., Zeng, J., Mann, K., & Johnson, N. (2019). Fas Mutations in Non-Hodgkin's Lymphoma (NHL): Implications for Disease Progression and Therapeutic Resistance. Blood. https://doi.org/10.1182/blood-2019-130602.*
50 50
## FAS Expression
51 51
![image](images/gene_expression/FAS_by_pathology.svg)
52
+<!-- ORIGIN: schollMutationsRegionFAS2007 -->
FAT4.md
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@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
39 39
![image](images/proteinpaint/FAT4.svg)
40 40
## FAT4 Expression
41 41
![image](images/gene_expression/FAT4_by_pathology.svg)
42
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
FBXO11.md
... ...
@@ -69,3 +69,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
69 69
5. *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. doi: 10.1038/s41375-021-01251-z. Epub 2021 May 5. PMID: 33953289; PMCID: PMC8257491.*
70 70
## FBXO11 Expression
71 71
![image](images/gene_expression/FBXO11_by_pathology.svg)
72
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
FNDC1.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
37 37
![image](images/proteinpaint/FNDC1.svg)
38 38
## FNDC1 Expression
39 39
![image](images/gene_expression/FNDC1_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
FOXC1.md
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
43 43
1. *Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407. doi: 10.1056/NEJMoa1801445. PMID: 29641966; PMCID: PMC6010183.*
44 44
45 45
<!-- FLAGGED FOR TIER 2 -->
46
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
FOXO1.md
... ...
@@ -78,3 +78,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
78 78
5. *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.*
79 79
## FOXO1 Expression
80 80
![image](images/gene_expression/FOXO1_by_pathology.svg)
81
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
FOXP1.md
... ...
@@ -48,3 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
48 48
![image](images/proteinpaint/FOXP1.svg)
49 49
## FOXP1 Expression
50 50
![image](images/gene_expression/FOXP1_by_pathology.svg)
51
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
FUBP1.md
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
43 43
![image](images/proteinpaint/FUBP1.svg)
44 44
## FUBP1 Expression
45 45
![image](images/gene_expression/FUBP1_by_pathology.svg)
46
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
FUT5.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
37 37
![image](images/proteinpaint/FUT5.svg)
38 38
## FUT5 Expression
39 39
![image](images/gene_expression/FUT5_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
GABRA2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
![image](images/proteinpaint/GABRA2.svg)
38 38
## GABRA2 Expression
39 39
![image](images/gene_expression/GABRA2_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
GAK.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
![image](images/proteinpaint/GAK.svg)
38 38
## GAK Expression
39 39
![image](images/gene_expression/GAK_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
GNA13.md
... ...
@@ -59,3 +59,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
59 59
2. *Muppidi JR, Schmitz R, Green JA, Xiao W, Larsen AB, Braun SE, An J, Xu Y, Rosenwald A, Ott G, Gascoyne RD, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Vaidehi N, Staudt LM, Cyster JG. Loss of signalling via Gα13 in germinal centre B-cell-derived lymphoma. Nature. 2014 Dec 11;516(7530):254-8. doi: 10.1038/nature13765. Epub 2014 Sep 28. PMID: 25274307; PMCID: PMC4267955.*
60 60
3. *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.*## GNA13 Expression
61 61
![image](images/gene_expression/GNA13_by_pathology.svg)
62
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
GNAI2.md
... ...
@@ -64,3 +64,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
64 64
1. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PMID: 23699601; PMCID: PMC3744992.*
65 65
## GNAI2 Expression
66 66
![image](images/gene_expression/GNAI2_by_pathology.svg)
67
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
GNAS.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
![image](images/proteinpaint/GNAS.svg)
38 38
## GNAS Expression
39 39
![image](images/gene_expression/GNAS_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
GOLGA5.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
![image](images/proteinpaint/GOLGA5.svg)
38 38
## GOLGA5 Expression
39 39
![image](images/gene_expression/GOLGA5_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
GPC5.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
![image](images/proteinpaint/GPC5.svg)
38 38
## GPC5 Expression
39 39
![image](images/gene_expression/GPC5_by_pathology.svg)
40
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
GRB2.md
... ...
@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
43 43
![image](images/proteinpaint/GRB2.svg)
44 44
## GRB2 Expression
45 45
![image](images/gene_expression/GRB2_by_pathology.svg)
46
+<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
GRHPR.md
... ...
@@ -48,3 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
48 48
1. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.*
49 49
## GRHPR Expression
50 50
![image](images/gene_expression/GRHPR_by_pathology.svg)
51
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
GSG2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37 37
![image](images/proteinpaint/GSG2.svg)
38 38
## GSG2 Expression
39 39
![image](images/gene_expression/GSG2_by_pathology.svg)
40
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
HDAC7.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
37 37
![image](images/proteinpaint/HDAC7.svg)
38 38
## HDAC7 Expression
39 39
![image](images/gene_expression/HDAC7_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
HIST1H1C.md
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
50 50
2. *Li H, Kaminski MS, Li Y, Yildiz M, Ouillette P, Jones S, Fox H, Jacobi K, Saiya-Cork K, Bixby D, Lebovic D, Roulston D, Shedden K, Sabel M, Marentette L, Cimmino V, Chang AE, Malek SN. Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma. Blood. 2014 Mar 6;123(10):1487-98. doi: 10.1182/blood-2013-05-500264. Epub 2014 Jan 16. PMID: 24435047; PMCID: PMC4729540.*
51 51
## HIST1H1C Expression
52 52
![image](images/gene_expression/HIST1H1C_by_pathology.svg)
53
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
HIST1H1D.md
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
44 44
![image](images/proteinpaint/HIST1H1D.svg)
45 45
## HIST1H1D Expression
46 46
![image](images/gene_expression/HIST1H1D_by_pathology.svg)
47
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
HIST1H2AC.md
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@@ -62,3 +62,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
62 62
![image](images/proteinpaint/HIST1H2AC.svg)
63 63
## HIST1H2AC Expression
64 64
![image](images/gene_expression/HIST1H2AC_by_pathology.svg)
65
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
HIST1H2AG.md
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@@ -52,3 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
52 52
![image](images/proteinpaint/HIST1H2AG.svg)
53 53
## HIST1H2AG Expression
54 54
![image](images/gene_expression/HIST1H2AG_by_pathology.svg)
55
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
HIST1H2BC.md
... ...
@@ -66,3 +66,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
66 66
![image](images/proteinpaint/HIST1H2BC.svg)
67 67
## HIST1H2BC Expression
68 68
![image](images/gene_expression/HIST1H2BC_by_pathology.svg)
69
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
HLA-DQA1.md
... ...
@@ -34,3 +34,4 @@ Mutations in this gene are relatively rare in DLBCL overall. *Without further su
34 34
35 35
<!-- FLAGGED FOR TIER 2 -->
36 36
<!-- ORPHANED -->
37
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
HNF1B.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
37 37
![image](images/proteinpaint/HNF1B.svg)
38 38
## HNF1B Expression
39 39
![image](images/gene_expression/HNF1B_by_pathology.svg)
40
+<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
HNRNPH1.md
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
50 50
2. *Coyle, K., Qureshi, Q., Pararajalingam, P., Thomas, N., Audas, T., & Morin, R. (2020). Perturbations in HNRNPH1 Splicing and Abundance Affect Global Splicing and Proliferation in Mantle Cell Lymphoma. Blood, 136, 23-24. https://doi.org/10.1182/BLOOD-2020-141389.*
51 51
52 52
<!-- NONCODING -->
53
+<!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 -->
HRAS.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
37 37
![image](images/proteinpaint/HRAS.svg)
38 38
## HRAS Expression
39 39
![image](images/gene_expression/HRAS_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
Home.md
... ...
@@ -6,10 +6,10 @@ of mutations in each gene can be found through the gene lists (below). Additiona
6 6
# B-cell Lymphoma gene lists
7 7
| entity | Tier 1 (high-confidence) | Tier 2 (low-confidence) |
8 8
| ----- | ----------- | ---------- |
9
-| DLBCL | [(156 genes)](tier1_dlbcl) |[(110 genes)](tier2_dlbcl) |
10
-| FL | [(66 genes)](tier1_fl) |[(51 genes)](tier2_fl) |
11
-| BL | [(30 genes)](tier1_bl) |[(188 genes)](tier2_bl) |
12
-| MCL | [(25 genes)](tier1_mcl) |[(30 genes)](tier2_mcl) |
9
+| DLBCL | [(152 genes)](tier1_dlbcl) |[(173 genes)](tier2_dlbcl) |
10
+| FL | [(65 genes)](tier1_fl) |[(50 genes)](tier2_fl) |
11
+| BL | [(29 genes)](tier1_bl) |[(188 genes)](tier2_bl) |
12
+| MCL | [(24 genes)](tier1_mcl) |[(29 genes)](tier2_mcl) |
13 13
14 14
# B-cell Lymphoma aSHM targets
15 15
[hg19 coordinates](ashm)
... ...
@@ -18,4 +18,4 @@ of mutations in each gene can be found through the gene lists (below). Additiona
18 18
19 19
![FOXO1](images/proteinpaint/FOXO1_NM_002015.svg)
20 20
21
-![expression](images/gene_expression/FOXO1_by_pathology.svg)
... ...
\ No newline at end of file
0
+![expression](images/gene_expression/FOXO1_by_pathology.svg)
ID3.md
... ...
@@ -48,3 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
48 48
![image](images/proteinpaint/ID3.svg)
49 49
## ID3 Expression
50 50
![image](images/gene_expression/ID3_by_pathology.svg)
51
+<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
IER2.md
... ...
@@ -28,3 +28,4 @@
28 28
> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29 29
## IER2 Expression
30 30
![image](images/gene_expression/IER2_by_pathology.svg)
31
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
IFNGR1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
37 37
![image](images/proteinpaint/IFNGR1.svg)
38 38
## IFNGR1 Expression
39 39
![image](images/gene_expression/IFNGR1_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
IKBKB.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
37 37
![image](images/proteinpaint/IKBKB.svg)
38 38
## IKBKB Expression
39 39
![image](images/gene_expression/IKBKB_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
IKBKE.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
37 37
![image](images/proteinpaint/IKBKE.svg)
38 38
## IKBKE Expression
39 39
![image](images/gene_expression/IKBKE_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
IKZF3.md
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@@ -73,3 +73,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
73 73
1. *Lazarian, G., Yin, S., Hacken, E., Sewastianik, T., Uduman, M., Font-Tello, A., Gohil, S., Li, S., Kim, E., Joyal, H., Billington, L., Witten, E., Zheng, M., Huang, T., Severgnini, M., Lefebvre, V., Rassenti, L., Gutierrez, C., Georgopoulos, K., Ott, C., Wang, L., Kipps, T., Burger, J., Livak, K., Neuberg, D., Baran-Marszak, F., Cymbalista, F., Carrasco, R., & Wu, C. (2021). A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation.. Cancer cell, 39 3, 380-393.e8 . https://doi.org/10.1016/j.ccell.2021.02.003.*
74 74
## IKZF3 Expression
75 75
![image](images/gene_expression/IKZF3_by_pathology.svg)
76
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
IL4R.md
... ...
@@ -54,3 +54,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
54 54
2. *Viganò E, Gunawardana J, Mottok A, Van Tol T, Mak K, Chan FC, Chong L, Chavez E, Woolcock B, Takata K, Twa D, Shulha HP, Telenius A, Kutovaya O, Hung SS, Healy S, Ben-Neriah S, Leroy K, Gaulard P, Diepstra A, Kridel R, Savage KJ, Rimsza L, Gascoyne R, Steidl C. Somatic IL4R mutations in primary mediastinal large B-cell lymphoma lead to constitutive JAK-STAT signaling activation. Blood. 2018 May 3;131(18):2036-2046. doi: 10.1182/blood-2017-09-808907. Epub 2018 Feb 21. PMID: 29467182.*
55 55
## IL4R Expression
56 56
![image](images/gene_expression/IL4R_by_pathology.svg)
57
+<!-- ORIGIN: dunsCharacterizationDLBCLPMBL2021b -->
IL6.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
37 37
![image](images/proteinpaint/IL6.svg)
38 38
## IL6 Expression
39 39
![image](images/gene_expression/IL6_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
INO80.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
37 37
![image](images/proteinpaint/INO80.svg)
38 38
## INO80 Expression
39 39
![image](images/gene_expression/INO80_by_pathology.svg)
40
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
IRF1.md
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@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
42 42
![image](images/proteinpaint/IRF1.svg)
43 43
## IRF1 Expression
44 44
![image](images/gene_expression/IRF1_by_pathology.svg)
45
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
IRF4.md
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@@ -60,3 +60,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
60 60
## References
61 61
1. *Hans CP, Weisenburger DD, Greiner TC, Gascoyne RD, Delabie J, Ott G, Müller-Hermelink HK, Campo E, Braziel RM, Jaffe ES, Pan Z, Farinha P, Smith LM, Falini B, Banham AH, Rosenwald A, Staudt LM, Connors JM, Armitage JO, Chan WC. Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray. Blood. 2004 Jan 1;103(1):275-82. doi: 10.1182/blood-2003-05-1545. Epub 2003 Sep 22. PMID: 14504078.*
62 62
2. *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.*
63
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
IRF8.md
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@@ -68,3 +68,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
68 68
3. *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.*
69 69
## IRF8 Expression
70 70
![image](images/gene_expression/IRF8_by_pathology.svg)
71
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
ITPKB.md
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@@ -55,3 +55,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
55 55
1. *Mareschal S, Dubois S, Viailly PJ, Bertrand P, Bohers E, Maingonnat C, Jaïs JP, Tesson B, Ruminy P, Peyrouze P, Copie-Bergman C, Fest T, Jo Molina T, Haioun C, Salles G, Tilly H, Lecroq T, Leroy K, Jardin F. Whole exome sequencing of relapsed/refractory patients expands the repertoire of somatic mutations in diffuse large B-cell lymphoma. Genes Chromosomes Cancer. 2016 Mar;55(3):251-67. doi: 10.1002/gcc.22328. Epub 2015 Nov 26. PMID: 26608593.*
56 56
## ITPKB Expression
57 57
![image](images/gene_expression/ITPKB_by_pathology.svg)
58
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
JAK1.md
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@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/J
43 43
![image](images/proteinpaint/JAK1.svg)
44 44
## JAK1 Expression
45 45
![image](images/gene_expression/JAK1_by_pathology.svg)
46
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
JAK3.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/J
37 37
![image](images/proteinpaint/JAK3.svg)
38 38
## JAK3 Expression
39 39
![image](images/gene_expression/JAK3_by_pathology.svg)
40
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
JUNB.md
... ...
@@ -49,3 +49,4 @@ Kostiantyn Dreval, Manuela Cruz, Christopher Rushton, Nina Liuta, Houman Layegh
49 49
bioRxiv 2023.11.21.567983; doi: https://doi.org/10.1101/2023.11.21.567983*
50 50
## JUNB Expression
51 51
![image](images/gene_expression/JUNB_by_pathology.svg)
52
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
KCMF1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
37 37
![image](images/proteinpaint/KCMF1.svg)
38 38
## KCMF1 Expression
39 39
![image](images/gene_expression/KCMF1_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
KLF2.md
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@@ -61,3 +61,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
61 61
2. *Clipson, A., Wang, M., Leval, L., Ashton-Key, M., Wotherspoon, A., Vassiliou, G., Bolli, N., Grove, C., Moody, S., Escudero-Ibarz, L., Gundem, G., Brügger, K., Xue, X., Mi, E., Bench, A., Scott, M., Liu, H., Follows, G., Robles, E., Martinez-Climent, J., Oscier, D., Watkins, A., & Du, M. (2014). KLF2 mutation is the most frequent somatic change in splenic marginal zone lymphoma and identifies a subset with distinct genotype. Leukemia, 29, 1177-1185. https://doi.org/10.1038/leu.2014.330.*
62 62
3. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.*## KLF2 Expression
63 63
![image](images/gene_expression/KLF2_by_pathology.svg)
64
+<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
KLHL14.md
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@@ -53,3 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
53 53
54 54
## KLHL14 Expression
55 55
![image](images/gene_expression/KLHL14_by_pathology.svg)
56
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
KLHL21.md
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
42 42
![image](images/proteinpaint/KLHL21.svg)
43 43
## KLHL21 Expression
44 44
![image](images/gene_expression/KLHL21_by_pathology.svg)
45
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
KLHL6.md
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@@ -77,3 +77,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
77 77
1. *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.*
78 78
2. *Choi, J., Zhou, N., & Busino, L. (2019). KLHL6 is a tumor suppressor gene in diffuse large B-cell lymphoma. Cell Cycle, 18, 249 - 256. https://doi.org/10.1080/15384101.2019.1568765.*## KLHL6 Expression
79 79
![image](images/gene_expression/KLHL6_by_pathology.svg)
80
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
KMT2C.md
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@@ -52,3 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
52 52
5. *Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988-96. doi: 10.1182/blood-2013-07-517177. Epub 2014 Mar 28. PMID: 24682267; PMCID: PMC4014841.*
53 53
## KMT2C Expression
54 54
![image](images/gene_expression/KMT2C_by_pathology.svg)
55
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
KMT2D.md
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@@ -54,3 +54,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
54 54
2. *You, H., Xu-Monette, Z., Wei, L., Nunns, H., Nagy, M., Bhagat, G., Fang, X., Zhu, F., Visco, C., Tzankov, A., Dybkaer, K., Chiu, A., Tam, W., Zu, Y., Hsi, E., Hagemeister, F., Huh, J., Ponzoni, M., Ferreri, A., Møller, M., Parsons, B., Krieken, J., Piris, M., Winter, J., Li, Y., Au, Q., Xu, B., Albitar, M., & Young, K. (2021). Genomic complexity is associated with epigenetic regulator mutations and poor prognosis in diffuse large B-cell lymphoma. Oncoimmunology, 10. https://doi.org/10.1080/2162402X.2021.1928365.*
55 55
3. *Rushton CK, Arthur SE, Alcaide M, Cheung M, Jiang A, Coyle KM, Cleary KLS, Thomas N, Hilton LK, Michaud N, Daigle S, Davidson J, Bushell K, Yu S, Rys RN, Jain M, Shepherd L, Marra MA, Kuruvilla J, Crump M, Mann K, Assouline S, Connors JM, Steidl C, Cragg MS, Scott DW, Johnson NA, Morin RD. Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma. Blood Adv. 2020 Jul 14;4(13):2886-2898. doi: 10.1182/bloodadvances.2020001696. PMID: 32589730; PMCID: PMC7362366.*
56 56
57
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
KRAS.md
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@@ -48,7 +48,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
48 48
49 49
![image](images/proteinpaint/KRAS.svg)
50 50
51
-## References
52
-1. Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.
53 51
## KRAS Expression
54 52
![image](images/gene_expression/KRAS_by_pathology.svg)
53
+
54
+## References
55
+1. *Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.*
56
+
57
+<!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->
LAMA5.md
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37 37
![image](images/proteinpaint/LAMA5.svg)
38 38
## LAMA5 Expression
39 39
![image](images/gene_expression/LAMA5_by_pathology.svg)
40
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
LCOR.md
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41 41
![image](images/proteinpaint/LCOR_hg38.svg)
42 42
## LCOR Expression
43 43
![image](images/gene_expression/LCOR_by_pathology.svg)
44
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
LIN54.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
37 37
![image](images/proteinpaint/LIN54.svg)
38 38
## LIN54 Expression
39 39
![image](images/gene_expression/LIN54_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
LPP.md
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50 50
![image](images/proteinpaint/LPP.svg)
51 51
## LPP Expression
52 52
![image](images/gene_expression/LPP_by_pathology.svg)
53
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
LRP12.md
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37 37
![image](images/proteinpaint/LRP12.svg)
38 38
## LRP12 Expression
39 39
![image](images/gene_expression/LRP12_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
LRRN3.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
37 37
![image](images/proteinpaint/LRRN3.svg)
38 38
## LRRN3 Expression
39 39
![image](images/gene_expression/LRRN3_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
MAGT1.md
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37 37
![image](images/proteinpaint/MAGT1.svg)
38 38
## MAGT1 Expression
39 39
![image](images/gene_expression/MAGT1_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MAP4K4.md
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37 37
![image](images/proteinpaint/MAP4K4.svg)
38 38
## MAP4K4 Expression
39 39
![image](images/gene_expression/MAP4K4_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MARK1.md
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37 37
![image](images/proteinpaint/MARK1.svg)
38 38
## MARK1 Expression
39 39
![image](images/gene_expression/MARK1_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MCL1.md
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53 53
## References
54 54
1. *Wenzel, S., Grau, M., Mavis, C., Hailfinger, S., Wolf, A., Madle, H., Deeb, G., Dörken, B., Thome, M., Lenz, P., Dirnhofer, S., Hernandez-Ilizaliturri, F., Tzankov, A., & Lenz, G. (2013). MCL1 is deregulated in subgroups of diffuse large B-cell lymphoma. Leukemia, 27, 1381-1390. https://doi.org/10.1038/leu.2012.367.*
55 55
2. *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 5;171(2):481-494.e15. doi: 10.1016/j.cell.2017.09.027. PMID: 28985567; PMCID: PMC5659841.*
56
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MECOM.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MECOM.svg)
38 38
## MECOM Expression
39 39
![image](images/gene_expression/MECOM_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MEF2B.md
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86 86
1. *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.*
87 87
88 88
89
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
MET.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MET.svg)
38 38
## MET Expression
39 39
![image](images/gene_expression/MET_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MGA.md
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
40 40
1. *Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1398-403. doi: 10.1073/pnas.1205299110. Epub 2013 Jan 4. PMID: 23292937; PMCID: PMC3557051.*
41 41
2. *Lee MJ, Koff JL, Switchenko JM, Jhaney CI, Harkins RA, Patel SP, Dave SS, Flowers CR. Genome-defined African ancestry is associated with distinct mutations and worse survival in patients with diffuse large B-cell lymphoma. Cancer. 2020 Aug 1;126(15):3493-3503. doi: 10.1002/cncr.32866. Epub 2020 May 29. PMID: 32469082; PMCID: PMC7494053.*
42 42
43
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
MIR142.md
... ...
@@ -28,3 +28,4 @@
28 28
> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2012 by [Kwanhian W](https://pubmed.ncbi.nlm.nih.gov/23342264)
29 29
## MIR142 Expression
30 30
![image](images/gene_expression/MIR142_by_pathology.svg)
31
+<!-- ORIGIN: kwanhianMicroRNA142Mutated202012b -->
MPDZ.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MPDZ.svg)
38 38
## MPDZ Expression
39 39
![image](images/gene_expression/MPDZ_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
MPEG1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
## References
38 38
1. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PMID: 23699601; PMCID: PMC3744992.*
39 39
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
MSH2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MSH2.svg)
38 38
## MSH2 Expression
39 39
![image](images/gene_expression/MSH2_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MSH6.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MSH6.svg)
38 38
## MSH6 Expression
39 39
![image](images/gene_expression/MSH6_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MTOR.md
... ...
@@ -53,4 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
53 53
54 54
## References
55 55
56
-1. *Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1398-403. doi: 10.1073/pnas.1205299110. Epub 2013 Jan 4. PMID: 23292937; PMCID: PMC3557051.*
... ...
\ No newline at end of file
0
+1. *Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1398-403. doi: 10.1073/pnas.1205299110. Epub 2013 Jan 4. PMID: 23292937; PMCID: PMC3557051.*<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
MYB.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MYB.svg)
38 38
## MYB Expression
39 39
![image](images/gene_expression/MYB_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
MYBPC2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MYBPC2.svg)
38 38
## MYBPC2 Expression
39 39
![image](images/gene_expression/MYBPC2_by_pathology.svg)
40
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
MYD88.md
... ...
@@ -48,3 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
48 48
![image](images/proteinpaint/MYD88.svg)
49 49
## MYD88 Expression
50 50
![image](images/gene_expression/MYD88_by_pathology.svg)
51
+<!-- ORIGIN: ngoOncogenicallyActiveMYD882011a -->
MYOM2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
37 37
![image](images/proteinpaint/MYOM2.svg)
38 38
## MYOM2 Expression
39 39
![image](images/gene_expression/MYOM2_by_pathology.svg)
40
+<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
N2RF2.md
... ...
@@ -31,3 +31,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
31 31
![image](images/proteinpaint/N2RF2.svg)
32 32
## N2RF2 Expression
33 33
![image](images/gene_expression/N2RF2_by_pathology.svg)
34
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
NANOG.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
![image](images/proteinpaint/NANOG.svg)
38 38
## NANOG Expression
39 39
![image](images/gene_expression/NANOG_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
NAV1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
![image](images/proteinpaint/NAV1.svg)
38 38
## NAV1 Expression
39 39
![image](images/gene_expression/NAV1_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
NCOR1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
![image](images/proteinpaint/NCOR1.svg)
38 38
## NCOR1 Expression
39 39
![image](images/gene_expression/NCOR1_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
NF1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
![image](images/proteinpaint/NF1.svg)
38 38
## NF1 Expression
39 39
![image](images/gene_expression/NF1_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
NFKB2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
![image](images/proteinpaint/NFKB2.svg)
38 38
## NFKB2 Expression
39 39
![image](images/gene_expression/NFKB2_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
NFKBIE.md
... ...
@@ -45,4 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
45 45
46 46
## References
47 47
1. *Mansouri, L., Noerenberg, D., Young, E., Mylonas, E., Abdulla, M., Frick, M., Asmar, F., Ljungström, V., Schneider, M., Yoshida, K., Skaftason, A., Pandzic, T., González, B., Tasidou, A., Waldhueter, N., Rivas-Delgado, A., Angelopoulou, M., Ziepert, M., Arends, C., Couronné, L., Lenze, D., Baldus, C., Bastard, C., Okosun, J., Fitzgibbon, J., Dörken, B., Drexler, H., Roos-Weil, D., Schmitt, C., Munch-Petersen, H., Zenz, T., Hansmann, M., Strefford, J., Enblad, G., Bernard, O., Ralfkiaer, E., Erlanson, M., Korkolopoulou, P., Hultdin, M., Papadaki, T., Grønbæk, K., López-Guillermo, A., Ogawa, S., Küppers, R., Stamatopoulos, K., Stavroyianni, N., Kanellis, G., Rosenwald, A., Campo, E., Amini, R., Ott, G., Vassilakopoulos, T., Hummel, M., Rosenquist, R., & Damm, F. (2016). Frequent NFKBIE deletions are associated with poor outcome in primary mediastinal B-cell lymphoma.. Blood, 128 23, 2666-2670 . https://doi.org/10.1182/BLOOD-2016-03-704528.*
48
-2. *Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572-584. doi: 10.1182/blood.2019002385. PMID: 32160292; PMCID: PMC7440974.*
... ...
\ No newline at end of file
0
+2. *Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572-584. doi: 10.1182/blood.2019002385. PMID: 32160292; PMCID: PMC7440974.*<!-- ORIGIN: morinGeneticLandscapesRelapsed2016 -->
NFKBIZ.md
... ...
@@ -48,3 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
48 48
1. *Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. doi: 10.1038/s41467-018-06354-3. PMID: 30275490; PMCID: PMC6167379.*
49 49
50 50
<!-- NONCODING -->
51
+<!-- ORIGIN: morinGeneticLandscapesRelapsed2016 -->
NLRP5.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
![image](images/proteinpaint/NLRP5.svg)
38 38
## NLRP5 Expression
39 39
![image](images/gene_expression/NLRP5_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
NLRP8.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
37 37
![image](images/proteinpaint/NLRP8.svg)
38 38
## NLRP8 Expression
39 39
![image](images/gene_expression/NLRP8_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
NOL9.md
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
42 42
![image](images/proteinpaint/NOL9.svg)
43 43
## NOL9 Expression
44 44
![image](images/gene_expression/NOL9_by_pathology.svg)
45
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
NOTCH1.md
... ...
@@ -49,3 +49,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
49 49
![image](images/proteinpaint/NOTCH1.svg)
50 50
## NOTCH1 Expression
51 51
![image](images/gene_expression/NOTCH1_by_pathology.svg)
52
+<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
NOTCH2.md
... ...
@@ -48,3 +48,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
48 48
![image](images/proteinpaint/NOTCH2.svg)
49 49
## NOTCH2 Expression
50 50
![image](images/gene_expression/NOTCH2_by_pathology.svg)
51
+<!-- ORIGIN: troenNOTCH2MutationsMarginal2008 -->
ODZ3.md
... ...
@@ -24,3 +24,4 @@
24 24
> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
25 25
## ODZ3 Expression
26 26
![image](images/gene_expression/ODZ3_by_pathology.svg)
27
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
OSBPL10.md
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/O
45 45
![image](images/proteinpaint/OSBPL10.svg)
46 46
## OSBPL10 Expression
47 47
![image](images/gene_expression/OSBPL10_by_pathology.svg)
48
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
P2RX5.md
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
42 42
![image](images/proteinpaint/P2RX5.svg)
43 43
## P2RX5 Expression
44 44
![image](images/gene_expression/P2RX5_by_pathology.svg)
45
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PAPOLG.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PAPOLG.svg)
38 38
## PAPOLG Expression
39 39
![image](images/gene_expression/PAPOLG_by_pathology.svg)
40
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
PASK.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PASK.svg)
38 38
## PASK Expression
39 39
![image](images/gene_expression/PASK_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PAX5.md
... ...
@@ -46,3 +46,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
46 46
![image](images/proteinpaint/PAX5.svg)
47 47
## PAX5 Expression
48 48
![image](images/gene_expression/PAX5_by_pathology.svg)
49
+<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
PCDHB11.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PCDHB11.svg)
38 38
## PCDHB11 Expression
39 39
![image](images/gene_expression/PCDHB11_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PCLO.md
... ...
@@ -1,4 +1,5 @@
1 1
# PCLO
2
+## Overview
2 3
3 4
## Relevance tier by entity
4 5
... ...
@@ -26,10 +27,6 @@
26 27
|FL |No |No |0.000 |0.000 |
27 28
28 29
29
-> [!NOTE]
30
-> First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
31
-
32
-
33 30
## PCLO Hotspots
34 31
35 32
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -45,5 +42,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
45 42
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCLO.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCLO_hg38.html)
46 43
47 44
![image](images/proteinpaint/PCLO.svg)
45
+
48 46
## PCLO Expression
49 47
![image](images/gene_expression/PCLO_by_pathology.svg)
48
+
49
+## References
50
+1. *Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.*
51
+
52
+
53
+<!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->
PDE4DIP.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PDE4DIP.svg)
38 38
## PDE4DIP Expression
39 39
![image](images/gene_expression/PDE4DIP_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
PDS5B.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 39
![image](images/proteinpaint/PDS5B.svg)
40 40
## PDS5B Expression
41 41
![image](images/gene_expression/PDS5B_by_pathology.svg)
42
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PHF6.md
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
41 41
![image](images/proteinpaint/PHF6.svg)
42 42
## PHF6 Expression
43 43
![image](images/gene_expression/PHF6_by_pathology.svg)
44
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
PIK3R1.md
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
41 41
![image](images/proteinpaint/PIK3R1.svg)
42 42
## PIK3R1 Expression
43 43
![image](images/gene_expression/PIK3R1_by_pathology.svg)
44
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
PIM1.md
... ...
@@ -75,3 +75,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
75 75
![image](images/proteinpaint/PIM1.svg)
76 76
## PIM1 Expression
77 77
![image](images/gene_expression/PIM1_by_pathology.svg)
78
+<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
PIM2.md
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
41 41
![image](images/proteinpaint/PIM2.svg)
42 42
## PIM2 Expression
43 43
![image](images/gene_expression/PIM2_by_pathology.svg)
44
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
PKD1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PKD1.svg)
38 38
## PKD1 Expression
39 39
![image](images/gene_expression/PKD1_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PNPO.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PNPO.svg)
38 38
## PNPO Expression
39 39
![image](images/gene_expression/PNPO_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
POGZ.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/POGZ.svg)
38 38
## POGZ Expression
39 39
![image](images/gene_expression/POGZ_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PPP1R9B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|DLBCL | 2 | low-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -30,5 +30,9 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
30 30
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PPP1R9B.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PPP1R9B_hg38.html)
31 31
32 32
![image](images/proteinpaint/PPP1R9B.svg)
33
+
33 34
## PPP1R9B Expression
34 35
![image](images/gene_expression/PPP1R9B_by_pathology.svg)
36
+
37
+<!-- FLAGGED FOR TIER 2 -->
38
+
PRDM1.md
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@@ -53,3 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
53 53
![image](images/proteinpaint/PRDM1.svg)
54 54
## PRDM1 Expression
55 55
![image](images/gene_expression/PRDM1_by_pathology.svg)
56
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PRKCB.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PRKCB.svg)
38 38
## PRKCB Expression
39 39
![image](images/gene_expression/PRKCB_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PRKDC.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 39
![image](images/proteinpaint/PRKDC.svg)
40 40
## PRKDC Expression
41 41
![image](images/gene_expression/PRKDC_by_pathology.svg)
42
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
PRPS1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PRPS1.svg)
38 38
## PRPS1 Expression
39 39
![image](images/gene_expression/PRPS1_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
PTPN23.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PTPN23.svg)
38 38
## PTPN23 Expression
39 39
![image](images/gene_expression/PTPN23_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
PTPN6.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PTPN6.svg)
38 38
## PTPN6 Expression
39 39
![image](images/gene_expression/PTPN6_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
PTPRK.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
![image](images/proteinpaint/PTPRK.svg)
38 38
## PTPRK Expression
39 39
![image](images/gene_expression/PTPRK_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
RAC2.md
... ...
@@ -49,3 +49,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
49 49
![image](images/proteinpaint/RAC2.svg)
50 50
## RAC2 Expression
51 51
![image](images/gene_expression/RAC2_by_pathology.svg)
52
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
RAD9A.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
![image](images/proteinpaint/RAD9A.svg)
38 38
## RAD9A Expression
39 39
![image](images/gene_expression/RAD9A_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
RARA.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
![image](images/proteinpaint/RARA.svg)
38 38
## RARA Expression
39 39
![image](images/gene_expression/RARA_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
RB1.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
39 39
![image](images/proteinpaint/RB1.svg)
40 40
## RB1 Expression
41 41
![image](images/gene_expression/RB1_by_pathology.svg)
42
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
RFTN1.md
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
42 42
![image](images/proteinpaint/RFTN1.svg)
43 43
## RFTN1 Expression
44 44
![image](images/gene_expression/RFTN1_by_pathology.svg)
45
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
RHOA.md
... ...
@@ -52,3 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
52 52
![image](images/proteinpaint/RHOA.svg)
53 53
## RHOA Expression
54 54
![image](images/gene_expression/RHOA_by_pathology.svg)
55
+<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
RRAGC.md
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@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
39 39
![image](images/proteinpaint/RRAGC.svg)
40 40
## RRAGC Expression
41 41
![image](images/gene_expression/RRAGC_by_pathology.svg)
42
+<!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->
RUNX1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
37 37
![image](images/proteinpaint/RUNX1.svg)
38 38
## RUNX1 Expression
39 39
![image](images/gene_expression/RUNX1_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
S1PR2.md
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
50 50
![image](images/proteinpaint/S1PR2.svg)
51 51
## S1PR2 Expression
52 52
![image](images/gene_expression/S1PR2_by_pathology.svg)
53
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
SAMD9L.md
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@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/SAMD9L.svg)
38 38
## SAMD9L Expression
39 39
![image](images/gene_expression/SAMD9L_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
SARM1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/SARM1.svg)
38 38
## SARM1 Expression
39 39
![image](images/gene_expression/SARM1_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
SERPINA9.md
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
42 42
![image](images/proteinpaint/SERPINA9.svg)
43 43
## SERPINA9 Expression
44 44
![image](images/gene_expression/SERPINA9_by_pathology.svg)
45
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
SETD1B.md
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
44 44
![image](images/proteinpaint/SETD1B.svg)
45 45
## SETD1B Expression
46 46
![image](images/gene_expression/SETD1B_by_pathology.svg)
47
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
SETD5.md
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
40 40
![image](images/proteinpaint/SETD5.svg)
41 41
## SETD5 Expression
42 42
![image](images/gene_expression/SETD5_by_pathology.svg)
43
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
SGK1.md
... ...
@@ -52,3 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
52 52
53 53
## SGK1 Expression
54 54
![image](images/gene_expression/SGK1_by_pathology.svg)
55
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
SIAH2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/SIAH2.svg)
38 38
## SIAH2 Expression
39 39
![image](images/gene_expression/SIAH2_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
SLC34A2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/SLC34A2.svg)
38 38
## SLC34A2 Expression
39 39
![image](images/gene_expression/SLC34A2_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
SMARCA4.md
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
45 45
![image](images/proteinpaint/SMARCA4.svg)
46 46
## SMARCA4 Expression
47 47
![image](images/gene_expression/SMARCA4_by_pathology.svg)
48
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
SMEK1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/SMEK1.svg)
38 38
## SMEK1 Expression
39 39
![image](images/gene_expression/SMEK1_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
SOCS1.md
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
45 45
![image](images/proteinpaint/SOCS1.svg)
46 46
## SOCS1 Expression
47 47
![image](images/gene_expression/SOCS1_by_pathology.svg)
48
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
SPEN.md
... ...
@@ -42,3 +42,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
42 42
![image](images/proteinpaint/SPEN.svg)
43 43
## SPEN Expression
44 44
![image](images/gene_expression/SPEN_by_pathology.svg)
45
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
SRRM2.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
39 39
![image](images/proteinpaint/SRRM2.svg)
40 40
## SRRM2 Expression
41 41
![image](images/gene_expression/SRRM2_by_pathology.svg)
42
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
STAT3.md
... ...
@@ -49,3 +49,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
49 49
![image](images/proteinpaint/STAT3.svg)
50 50
## STAT3 Expression
51 51
![image](images/gene_expression/STAT3_by_pathology.svg)
52
+<!-- ORIGIN: ohgamiSTAT3MutationsAre2014 -->
STAT5B.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/STAT5B.svg)
38 38
## STAT5B Expression
39 39
![image](images/gene_expression/STAT5B_by_pathology.svg)
40
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
STAT6.md
... ...
@@ -66,3 +66,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
66 66
1. *Morin RD, Assouline S, Alcaide M, Mohajeri A, Johnston RL, Chong L, Grewal J, Yu S, Fornika D, Bushell K, Nielsen TH, Petrogiannis-Haliotis T, Crump M, Tosikyan A, Grande BM, MacDonald D, Rousseau C, Bayat M, Sesques P, Froment R, Albuquerque M, Monczak Y, Oros KK, Greenwood C, Riazalhosseini Y, Arseneault M, Camlioglu E, Constantin A, Pan-Hammarstrom Q, Peng R, Mann KK, Johnson NA. Genetic Landscapes of Relapsed and Refractory Diffuse Large B-Cell Lymphomas. Clin Cancer Res. 2016 May 1;22(9):2290-300. doi: 10.1158/1078-0432.CCR-15-2123. Epub 2015 Dec 8. PMID: 26647218.*
67 67
## STAT6 Expression
68 68
![image](images/gene_expression/STAT6_by_pathology.svg)
69
+<!-- ORIGIN: morinGeneticLandscapesRelapsed2016 -->
SYK.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/SYK.svg)
38 38
## SYK Expression
39 39
![image](images/gene_expression/SYK_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
SYPL1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37 37
![image](images/proteinpaint/SYPL1.svg)
38 38
## SYPL1 Expression
39 39
![image](images/gene_expression/SYPL1_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
TAF1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
![image](images/proteinpaint/TAF1.svg)
38 38
## TAF1 Expression
39 39
![image](images/gene_expression/TAF1_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
TAP1.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
![image](images/proteinpaint/TAP1.svg)
38 38
## TAP1 Expression
39 39
![image](images/gene_expression/TAP1_by_pathology.svg)
40
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
TBC1D4.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
39 39
![image](images/proteinpaint/TBC1D4.svg)
40 40
## TBC1D4 Expression
41 41
![image](images/gene_expression/TBC1D4_by_pathology.svg)
42
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
TBL1XR1.md
... ...
@@ -56,3 +56,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
56 56
![image](images/proteinpaint/TBL1XR1.svg)
57 57
## TBL1XR1 Expression
58 58
![image](images/gene_expression/TBL1XR1_by_pathology.svg)
59
+<!-- ORIGIN: mareschalWholeExomeSequencing2016 -->
TET2.md
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
41 41
![image](images/proteinpaint/TET2.svg)
42 42
## TET2 Expression
43 43
![image](images/gene_expression/TET2_by_pathology.svg)
44
+<!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a -->
TGFBR2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
![image](images/proteinpaint/TGFBR2.svg)
38 38
## TGFBR2 Expression
39 39
![image](images/gene_expression/TGFBR2_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
TIPARP.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
![image](images/proteinpaint/TIPARP.svg)
38 38
## TIPARP Expression
39 39
![image](images/gene_expression/TIPARP_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
TLR2.md
... ...
@@ -46,3 +46,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
46 46
![image](images/proteinpaint/TLR2.svg)
47 47
## TLR2 Expression
48 48
![image](images/gene_expression/TLR2_by_pathology.svg)
49
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
TMEM30A.md
... ...
@@ -53,3 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
53 53
1. *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.*
54 54
## TMEM30A Expression
55 55
![image](images/gene_expression/TMEM30A_by_pathology.svg)
56
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
TMSB4X.md
... ...
@@ -50,3 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
50 50
![image](images/proteinpaint/TMSB4X.svg)
51 51
## TMSB4X Expression
52 52
![image](images/gene_expression/TMSB4X_by_pathology.svg)
53
+<!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a -->
TNFAIP3.md
... ...
@@ -53,3 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
53 53
1.
54 54
2. *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.*## TNFAIP3 Expression
55 55
![image](images/gene_expression/TNFAIP3_by_pathology.svg)
56
+<!-- ORIGIN: compagnoMutationsMultipleGenes2009a -->
TNFRSF14.md
... ...
@@ -64,3 +64,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
64 64
## References
65 65
1. *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, Ch$
66 66
67
+<!-- ORIGIN: cheungAcquiredTNFRSF14Mutations2010a -->
TOX.md
... ...
@@ -47,3 +47,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
47 47
![image](images/proteinpaint/TOX.svg)
48 48
## TOX Expression
49 49
![image](images/gene_expression/TOX_by_pathology.svg)
50
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
TRAF3.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
37 37
![image](images/proteinpaint/TRAF3.svg)
38 38
## TRAF3 Expression
39 39
![image](images/gene_expression/TRAF3_by_pathology.svg)
40
+<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
TRAF6.md
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
45 45
![image](images/proteinpaint/TRAF6.svg)
46 46
## TRAF6 Expression
47 47
![image](images/gene_expression/TRAF6_by_pathology.svg)
48
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
UBE2A.md
... ...
@@ -38,3 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
38 38
![image](images/proteinpaint/UBE2A.svg)
39 39
## UBE2A Expression
40 40
![image](images/gene_expression/UBE2A_by_pathology.svg)
41
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
UBR5.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
39 39
![image](images/proteinpaint/UBR5.svg)
40 40
## UBR5 Expression
41 41
![image](images/gene_expression/UBR5_by_pathology.svg)
42
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
UNC5B.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
37 37
![image](images/proteinpaint/UNC5B.svg)
38 38
## UNC5B Expression
39 39
![image](images/gene_expression/UNC5B_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
UNC5D.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|DLBCL | 2 |low-confidence DLBCL gene|
8 8
9 9
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 10
... ...
@@ -32,5 +32,8 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
32 32
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/UNC5D.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/UNC5D_hg38.html)
33 33
34 34
![image](images/proteinpaint/UNC5D.svg)
35
+
35 36
## UNC5D Expression
36 37
![image](images/gene_expression/UNC5D_by_pathology.svg)
38
+
39
+<!-- FLAGGED FOR TIER 2 -->
... ...
\ No newline at end of file
WAC.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
37 37
![image](images/proteinpaint/WAC.svg)
38 38
## WAC Expression
39 39
![image](images/gene_expression/WAC_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
WDFY3.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
37 37
![image](images/proteinpaint/WDFY3.svg)
38 38
## WDFY3 Expression
39 39
![image](images/gene_expression/WDFY3_by_pathology.svg)
40
+<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
WEE1.md
... ...
@@ -51,3 +51,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
51 51
![image](images/proteinpaint/WEE1.svg)
52 52
## WEE1 Expression
53 53
![image](images/gene_expression/WEE1_by_pathology.svg)
54
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
WNK1.md
... ...
@@ -47,3 +47,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
47 47
![image](images/proteinpaint/WNK1.svg)
48 48
## WNK1 Expression
49 49
![image](images/gene_expression/WNK1_by_pathology.svg)
50
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
XBP1.md
... ...
@@ -39,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/X
39 39
![image](images/proteinpaint/XBP1.svg)
40 40
## XBP1 Expression
41 41
![image](images/gene_expression/XBP1_by_pathology.svg)
42
+
43
+<!-- FLAGGED FOR REMOVAL -->
... ...
\ No newline at end of file
XPO1.md
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/X
44 44
![image](images/proteinpaint/XPO1.svg)
45 45
## XPO1 Expression
46 46
![image](images/gene_expression/XPO1_by_pathology.svg)
47
+<!-- ORIGIN: mareschalWholeExomeSequencing2016 -->
YY1.md
... ...
@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Y
39 39
![image](images/proteinpaint/YY1.svg)
40 40
## YY1 Expression
41 41
![image](images/gene_expression/YY1_by_pathology.svg)
42
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ZBTB7A.md
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@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
41 41
![image](images/proteinpaint/ZBTB7A.svg)
42 42
## ZBTB7A Expression
43 43
![image](images/gene_expression/ZBTB7A_by_pathology.svg)
44
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ZCCHC7.md
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@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
45 45
![image](images/proteinpaint/ZCCHC7.svg)
46 46
## ZCCHC7 Expression
47 47
![image](images/gene_expression/ZCCHC7_by_pathology.svg)
48
+<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
ZEB2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
![image](images/proteinpaint/ZEB2.svg)
38 38
## ZEB2 Expression
39 39
![image](images/gene_expression/ZEB2_by_pathology.svg)
40
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
ZFAT.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
![image](images/proteinpaint/ZFAT.svg)
38 38
## ZFAT Expression
39 39
![image](images/gene_expression/ZFAT_by_pathology.svg)
40
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ZFP36L1.md
... ...
@@ -45,3 +45,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
45 45
![image](images/proteinpaint/ZFP36L1.svg)
46 46
## ZFP36L1 Expression
47 47
![image](images/gene_expression/ZFP36L1_by_pathology.svg)
48
+<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
ZFX.md
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
40 40
![image](images/proteinpaint/ZFX.svg)
41 41
## ZFX Expression
42 42
![image](images/gene_expression/ZFX_by_pathology.svg)
43
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ZNF217.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
![image](images/proteinpaint/ZNF217.svg)
38 38
## ZNF217 Expression
39 39
![image](images/gene_expression/ZNF217_by_pathology.svg)
40
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
ZNF292.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
![image](images/proteinpaint/ZNF292.svg)
38 38
## ZNF292 Expression
39 39
![image](images/gene_expression/ZNF292_by_pathology.svg)
40
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
ZNF423.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
![image](images/proteinpaint/ZNF423.svg)
38 38
## ZNF423 Expression
39 39
![image](images/gene_expression/ZNF423_by_pathology.svg)
40
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
ZNF608.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
37 37
![image](images/proteinpaint/ZNF608.svg)
38 38
## ZNF608 Expression
39 39
![image](images/gene_expression/ZNF608_by_pathology.svg)
40
+<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
tier1_dlbcl.md
... ...
@@ -113,7 +113,6 @@
113 113
|1-a|[PIM2](PIM2)|3.44|[view](images/proteinpaint/PIM2.svg)|[view](images/proteinpaint/PIM2_NM_006875.svg)|
114 114
|1-a|[POU2AF1](POU2AF1)|5.16|[view](images/proteinpaint/POU2AF1.svg)|[view](images/proteinpaint/POU2AF1_NM_006235.svg)|
115 115
|1|[POU2F2](POU2F2)|5.93|[view](images/proteinpaint/POU2F2.svg)|[view](images/proteinpaint/POU2F2_NM_002698.svg)|
116
-|1|[PPP1R9B](PPP1R9B)|0.38|[view](images/proteinpaint/PPP1R9B.svg)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/PPP1R9B_protein.html)|
117 116
|1|[PRDM1](PRDM1)|6.88|[view](images/proteinpaint/PRDM1.svg)|[view](images/proteinpaint/PRDM1_NM_001198.svg)|
118 117
|1|[PRKDC](PRKDC)|2.68|[view](images/proteinpaint/PRKDC.svg)|[view](images/proteinpaint/PRKDC_NM_006904.svg)|
119 118
|1|[PTEN](PTEN)|3.82|[view](images/proteinpaint/PTEN.svg)|[view](images/proteinpaint/PTEN_NM_000314.svg)|
... ...
@@ -146,7 +145,6 @@
146 145
|1|[TRRAP](TRRAP)|2.87|[view](images/proteinpaint/TRRAP.svg)|[view](images/proteinpaint/TRRAP_NM_003496.svg)|
147 146
|1|[UBE2A](UBE2A)|4.21|[view](images/proteinpaint/UBE2A.svg)|[view](images/proteinpaint/UBE2A_NM_003336.svg)|
148 147
|1|[UNC5C](UNC5C)|3.44|[view](images/proteinpaint/UNC5C.svg)|[view](images/proteinpaint/UNC5C_NM_003728.svg)|
149
-|1|[UNC5D](UNC5D)|2.10|[view](images/proteinpaint/UNC5D.svg)|[view](images/proteinpaint/UNC5D_NM_080872.svg)|
150 148
|1|[USP7](USP7)|1.34|[view](images/proteinpaint/USP7.svg)|[view](images/proteinpaint/USP7_NM_003470.svg)|
151 149
|1|[VPS13B](VPS13B)|4.21|[view](images/proteinpaint/VPS13B.svg)|[view](images/proteinpaint/VPS13B_NM_152564.svg)|
152 150
|1-a|[WEE1](WEE1)|4.02|[view](images/proteinpaint/WEE1.svg)|[view](images/proteinpaint/WEE1_NM_003390.svg)|
tier2_dlbcl.md
... ...
@@ -106,6 +106,7 @@
106 106
|2|[ODZ3](ODZ3)|0.00|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/ODZ3.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/ODZ3_protein.html)|
107 107
|2-a|[P2RX5](P2RX5)|1.15|[view](images/proteinpaint/P2RX5.svg)|[view](images/proteinpaint/P2RX5_NM_002561.svg)|
108 108
|2|[PAPOLG](PAPOLG)|0.38|[view](images/proteinpaint/PAPOLG.svg)|[view](images/proteinpaint/PAPOLG_NM_022894.svg)|
109
+|2|[PPP1R9B](PPP1R9B)|0.38|[view](images/proteinpaint/PPP1R9B.svg)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/PPP1R9B_protein.html)|
109 110
|2|[PTPN23](PTPN23)|1.34|[view](images/proteinpaint/PTPN23.svg)|[view](images/proteinpaint/PTPN23_NM_015466.svg)|
110 111
|2|[PASK](PASK)|1.91|[view](images/proteinpaint/PASK.svg)|[view](images/proteinpaint/PASK_NM_015148.svg)|
111 112
|2-a|[PAX5](PAX5)|3.63|[view](images/proteinpaint/PAX5.svg)|[view](images/proteinpaint/PAX5_NM_016734.svg)|
... ...
@@ -128,7 +129,6 @@
128 129
|2|[RAC2](RAC2)|1.15|[view](images/proteinpaint/RAC2.svg)|[view](images/proteinpaint/RAC2_NM_002872.svg)|
129 130
|2|[RAD9A](RAD9A)|0.19|[view](images/proteinpaint/RAD9A.svg)|[view](images/proteinpaint/RAD9A_NM_004584.svg)|
130 131
|2|[RARA](RARA)|1.34|[view](images/proteinpaint/RARA.svg)|[view](images/proteinpaint/RARA_NM_000964.svg)|
131
-|2|[RCC](RCC)|0.00|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RCC.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RCC_protein.html)|
132 132
|2-a|[RFTN1](RFTN1)|4.59|[view](images/proteinpaint/RFTN1.svg)|[view](images/proteinpaint/RFTN1_NM_015150.svg)|
133 133
|2-a|[RHEX](RHEX)(C1orf186)|0.00|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RHEX.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RHEX_protein.html)|
134 134
|2-a|[RHOH](RHOH)|1.15|[view](images/proteinpaint/RHOH.svg)|[view](images/proteinpaint/RHOH_NM_004310.svg)|
... ...
@@ -161,6 +161,7 @@
161 161
|2-a|[UBE2J1](UBE2J1)|0.76|[view](images/proteinpaint/UBE2J1.svg)|[view](images/proteinpaint/UBE2J1_NM_016021.svg)|
162 162
|2|[UBR5](UBR5)|3.63|[view](images/proteinpaint/UBR5.svg)|[view](images/proteinpaint/UBR5_NM_015902.svg)|
163 163
|2|[UNC5B](UNC5B)|1.53|[view](images/proteinpaint/UNC5B.svg)|[view](images/proteinpaint/UNC5B_NM_170744.svg)|
164
+|2|[UNC5D](UNC5D)|2.10|[view](images/proteinpaint/UNC5D.svg)|[view](images/proteinpaint/UNC5D_NM_080872.svg)|
164 165
|2|[WAC](WAC)|2.68|[view](images/proteinpaint/WAC.svg)|[view](images/proteinpaint/WAC_NM_016628.svg)|
165 166
|2|[WDFY3](WDFY3)|4.21|[view](images/proteinpaint/WDFY3.svg)|[view](images/proteinpaint/WDFY3_NM_014991.svg)|
166 167
|2|[WNK1](WNK1)|4.59|[view](images/proteinpaint/WNK1.svg)|[view](images/proteinpaint/WNK1_NM_018979.svg)|