Changes in bc4f5dc: fix refs

				BCL10.md
			
          @@ -32,9 +32,6 @@ BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling an

           |FL    |No  |Yes                  | 0.000          |223.832         |

          -> [!NOTE]

          -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)

          -

            ## BCL10 Hotspots

           | Chromosome |Coordinate (hg19) | ref>alt | HGVSp | 

          @@ -51,10 +48,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ![image](images/proteinpaint/BCL10.svg)

          +## BCL10 Expression

          +

          +![image](images/gene_expression/BCL10_by_pathology.svg)

          +

           ## References

           1. *Luminari S, Intini D, Baldini L, Berti E, Bertoni F, Zucca E, Cro L, Maiolo AT, Cavalli F, Neri A. BCL10 gene mutations rarely occur in lymphoid malignancies. Leukemia. 2000 May;14(5):905-8. doi: 10.1038/sj.leu.2401747. PMID: 10803524.*

          -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

          -![image](images/gene_expression/BCL10_by_pathology.svg)

          +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.*

          +

           <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

				CD58.md
			
          @@ -31,10 +31,6 @@ CD58, also known as lymphocyte function-associated antigen 3 (LFA-3), is crucial

           |FL    |No  |Yes                  |0.00            |107.458         |

          -> [!NOTE]

          -> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CD58_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CD58_protein_hg38.html)

           ![image](images/proteinpaint/CD58_NM_001779.svg)

          @@ -43,9 +39,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/proteinpaint/CD58.svg)

          +## CD58 Expression

          +![image](images/gene_expression/CD58_by_pathology.svg)

          +

           ## References

           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.*

          -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

          -![image](images/gene_expression/CD58_by_pathology.svg)

          +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.*

           <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

				CD79B.md
			
          @@ -63,10 +63,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/proteinpaint/CD79B.svg)

          +## CD79B Expression

          +![image](images/gene_expression/CD79B_by_pathology.svg)

          +

           ## References

           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.*

           2. *Flümann R, Hansen J, Meinel J, Pfeiffer P, Goldfarb Wittkopf H, Lütz A, Wirtz J, Möllmann M, Zhou T, Tabatabai A, Lohmann T, Jauch M, Beleggia F, Pelzer B, Ullrich F, Höfmann S, Arora A, Persigehl T, Büttner R, von Tresckow B, Klein S, Jachimowicz RD, Reinhardt HC, Knittel G. An inducible Cd79b mutation confers ibrutinib sensitivity in mouse models of Myd88-driven diffuse large B-cell lymphoma. Blood Adv. 2024 Mar 12;8(5):1063-1074. doi: 10.1182/bloodadvances.2023011213. PMID: 38060829; PMCID: PMC10907402.*

           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.*

          -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

          -![image](images/gene_expression/CD79B_by_pathology.svg)

          +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.*

           <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

				CDKN2A.md
			
          @@ -32,10 +32,6 @@ Although CDKN2A aberrations are common in DLBCL, this gene is predominantly affe

           |DLBCL |CDKN2A.p16INK4a|No  |Yes                  | 5.631          |442.466         |

           |FL    |CDKN2A.p16INK4a|No  |No                   | 0.000          |159.196         |

          -

          -> [!NOTE]

          -> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)

          -

           ## CDKN2A Hotspots

           | Chromosome |Coordinate (hg19) | ref>alt | HGVSp | 

          @@ -50,7 +46,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/proteinpaint/CDKN2A.svg)

          -## References

          -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

          +## CDKN2A Expression

          +

           ![image](images/gene_expression/CDKN2A_by_pathology.svg)

          +

          +## References

          +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.*

          +

           <!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->

				CIITA.md
			
          @@ -43,9 +43,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/proteinpaint/CIITA.svg)

          +## CIITA Expression

          +![image](images/gene_expression/CIITA_by_pathology.svg)

          +

           ## References

           1. *Mottok, A., Woolcock, B., Chan, F., Tong, K., Chong, L., Farinha, P., Telenius, A., Chavez, E., Ramchandani, S., Drake, M., Boyle, M., Ben-Neriah, S., Scott, D., Rimsza, L., Siebert, R., Gascoyne, R., & Steidl, C. (2015). Genomic Alterations in CIITA Are Frequent in Primary Mediastinal Large B Cell Lymphoma and Are Associated with Diminished MHC Class II Expression.. Cell reports, 13 7, 1418-1431 . https://doi.org/10.1016/j.celrep.2015.10.008.*

           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*

          -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

          -![image](images/gene_expression/CIITA_by_pathology.svg)

          +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.*

          +

           <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

				EP300.md
			
          @@ -72,6 +72,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E

           ![image](images/proteinpaint/EP300.svg)

          +## EP300 Expression

          +![image](images/gene_expression/EP300_by_pathology.svg)

          +

           ## References

           1. *Pasqualucci, L., Dominguez-Sola, D., Chiarenza, A., Fabbri, G., Grunn, A., Trifonov, V., Kasper, L., Lerach, S., Tang, H., Ma, J., Rossi, D., Chadburn, A., Murty, V., Mullighan, C., Gaidano, G., Rabadán, R., Brindle, P., & Dalla-Favera, R. (2010). Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature, 471, 189 - 195. https://doi.org/10.1038/nature09730.*

          @@ -79,6 +82,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E

           3. *Nie M, Du L, Ren W, Joung J, Ye X, Shi X, Ciftci S, Liu D, Wu K, Zhang F, Pan-Hammarström Q. Genome-wide CRISPR screens reveal synthetic lethal interaction between CREBBP and EP300 in diffuse large B-cell lymphoma. Cell Death Dis. 2021 Apr 28;12(5):419. doi: 10.1038/s41419-021-03695-8. PMID: 33911074; PMCID: PMC8080727.*

          -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

          -![image](images/gene_expression/EP300_by_pathology.svg)

          +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.*

          +

           <!-- ORIGIN: pasqualucciInactivatingMutationsAcetyltransferase2011a -->

...	...	@@ -32,9 +32,6 @@ BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling an
32	32	\|FL \|No \|Yes \| 0.000 \|223.832 \|
33	33
34	34
35		-> [!NOTE]
36		-> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
37		-
38	35	## BCL10 Hotspots
39	36
40	37	\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
...	...	@@ -51,10 +48,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
51	48
52	49	![image](images/proteinpaint/BCL10.svg)
53	50
	51	+## BCL10 Expression
	52	+
	53	+![image](images/gene_expression/BCL10_by_pathology.svg)
	54	+
54	55	## References
55	56
56	57	1. Luminari S, Intini D, Baldini L, Berti E, Bertoni F, Zucca E, Cro L, Maiolo AT, Cavalli F, Neri A. BCL10 gene mutations rarely occur in lymphoid malignancies. Leukemia. 2000 May;14(5):905-8. doi: 10.1038/sj.leu.2401747. PMID: 10803524.
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		-![image](images/gene_expression/BCL10_by_pathology.svg)
	59	+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.
	60	+
60	61	<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -31,10 +31,6 @@ CD58, also known as lymphocyte function-associated antigen 3 (LFA-3), is crucial
31	31	\|FL \|No \|Yes \|0.00 \|107.458 \|
32	32
33	33
34		-> [!NOTE]
35		-> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
36		-
37		-
38	34	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CD58_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CD58_protein_hg38.html)
39	35
40	36	![image](images/proteinpaint/CD58_NM_001779.svg)
...	...	@@ -43,9 +39,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
43	39
44	40	![image](images/proteinpaint/CD58.svg)
45	41
	42	+## CD58 Expression
	43	+![image](images/gene_expression/CD58_by_pathology.svg)
	44	+
46	45	## References
47	46
48	47	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		-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		-![image](images/gene_expression/CD58_by_pathology.svg)
	48	+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.
51	49	<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -63,10 +63,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
63	63
64	64	![image](images/proteinpaint/CD79B.svg)
65	65
	66	+## CD79B Expression
	67	+![image](images/gene_expression/CD79B_by_pathology.svg)
	68	+
66	69	## References
67	70	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.
68	71	2. Flümann R, Hansen J, Meinel J, Pfeiffer P, Goldfarb Wittkopf H, Lütz A, Wirtz J, Möllmann M, Zhou T, Tabatabai A, Lohmann T, Jauch M, Beleggia F, Pelzer B, Ullrich F, Höfmann S, Arora A, Persigehl T, Büttner R, von Tresckow B, Klein S, Jachimowicz RD, Reinhardt HC, Knittel G. An inducible Cd79b mutation confers ibrutinib sensitivity in mouse models of Myd88-driven diffuse large B-cell lymphoma. Blood Adv. 2024 Mar 12;8(5):1063-1074. doi: 10.1182/bloodadvances.2023011213. PMID: 38060829; PMCID: PMC10907402.
69	72	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		-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		-![image](images/gene_expression/CD79B_by_pathology.svg)
	73	+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.
72	74	<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -32,10 +32,6 @@ Although CDKN2A aberrations are common in DLBCL, this gene is predominantly affe
32	32	\|DLBCL \|CDKN2A.p16INK4a\|No \|Yes \| 5.631 \|442.466 \|
33	33	\|FL \|CDKN2A.p16INK4a\|No \|No \| 0.000 \|159.196 \|
34	34
35		-
36		-> [!NOTE]
37		-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
38		-
39	35	## CDKN2A Hotspots
40	36
41	37	\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
...	...	@@ -50,7 +46,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
50	46
51	47	![image](images/proteinpaint/CDKN2A.svg)
52	48
53		-## References
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
	49	+## CDKN2A Expression
	50	+
55	51	![image](images/gene_expression/CDKN2A_by_pathology.svg)
	52	+
	53	+## References
	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.
	55	+
56	56	<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->

...	...	@@ -43,9 +43,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
43	43
44	44	![image](images/proteinpaint/CIITA.svg)
45	45
	46	+## CIITA Expression
	47	+![image](images/gene_expression/CIITA_by_pathology.svg)
	48	+
46	49	## References
47	50	1. Mottok, A., Woolcock, B., Chan, F., Tong, K., Chong, L., Farinha, P., Telenius, A., Chavez, E., Ramchandani, S., Drake, M., Boyle, M., Ben-Neriah, S., Scott, D., Rimsza, L., Siebert, R., Gascoyne, R., & Steidl, C. (2015). Genomic Alterations in CIITA Are Frequent in Primary Mediastinal Large B Cell Lymphoma and Are Associated with Diminished MHC Class II Expression.. Cell reports, 13 7, 1418-1431 . https://doi.org/10.1016/j.celrep.2015.10.008.
48	51	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		-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		-![image](images/gene_expression/CIITA_by_pathology.svg)
	52	+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.
	53	+
51	54	<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -72,6 +72,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
72	72
73	73	![image](images/proteinpaint/EP300.svg)
74	74
	75	+## EP300 Expression
	76	+![image](images/gene_expression/EP300_by_pathology.svg)
	77	+
75	78	## References
76	79	1. Pasqualucci, L., Dominguez-Sola, D., Chiarenza, A., Fabbri, G., Grunn, A., Trifonov, V., Kasper, L., Lerach, S., Tang, H., Ma, J., Rossi, D., Chadburn, A., Murty, V., Mullighan, C., Gaidano, G., Rabadán, R., Brindle, P., & Dalla-Favera, R. (2010). Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature, 471, 189 - 195. https://doi.org/10.1038/nature09730.
77	80
...	...	@@ -79,6 +82,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
79	82
80	83	3. Nie M, Du L, Ren W, Joung J, Ye X, Shi X, Ciftci S, Liu D, Wu K, Zhang F, Pan-Hammarström Q. Genome-wide CRISPR screens reveal synthetic lethal interaction between CREBBP and EP300 in diffuse large B-cell lymphoma. Cell Death Dis. 2021 Apr 28;12(5):419. doi: 10.1038/s41419-021-03695-8. PMID: 33911074; PMCID: PMC8080727.
81	84
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		-![image](images/gene_expression/EP300_by_pathology.svg)
	85	+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.
	86	+
84	87	<!-- ORIGIN: pasqualucciInactivatingMutationsAcetyltransferase2011a -->