Changes in 5b73fc5: fix

				DLBCL_genes.md
			
          @@ -260,7 +260,7 @@ link-citations: true

           |[MYBPC2](MYBPC2)|2|[@schmitzGeneticsPathogenesisDiffuse2018a]||

           |[MYO1E](MYO1E)|2, aSHM|||

           |[MYOM2](MYOM2)|2|[@pasqualucciAnalysisCodingGenome2011]||

          -|[N2RF2](N2RF2)|2|[@hubschmannMutationalMechanismsShaping2021b]||

          +|[NR2F2](N2RF2)|2|[@hubschmannMutationalMechanismsShaping2021b]||

           |[NANOG](NANOG)|2|[@chapuyMolecularSubtypesDiffuse2018b]||

           |[NAV1](NAV1)|2|[@chapuyMolecularSubtypesDiffuse2018b]||

           |[NCOA3](NCOA3)|2, aSHM|||

				N2RF2.md
			
          @@ -1,43 +0,0 @@

          -# N2RF2

          -

          -## History

          -Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>

          -

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2021-05-05 : Hübschmann : DLBCL

          -```

          -

          -## Relevance tier by entity

          -

          -|Entity|Tier|Description                              |

          -|:------:|:----:|-----------------------------------------|

          -|![DLBCL](images/icons/DLBCL_tier2.png) |2   |relevance in DLBCL not firmly established|

          -

          -## Mutation incidence in large patient cohorts (GAMBL reanalysis)

          -

          -|Entity|source        |frequency (%)|

          -|:------:|:--------------:|:-------------:|

          -|DLBCL |GAMBL genomes |NA           |

          -|DLBCL |Schmitz cohort|NA           |

          -|DLBCL |Reddy cohort  |NA           |

          -|DLBCL |Chapuy cohort |NA           |

          -

          -View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein_hg38.html)

          -

          -View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_hg38.html)

          -

          -![](images/proteinpaint/N2RF2.svg)

          -

          -## N2RF2 Expression

          -![](images/gene_expression/N2RF2_by_pathology.svg)

          -

          -

          -## References

          -1.  Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491

          -

          -

          -<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->

          -<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->

				NR2F2.md
			
          @@ -0,0 +1,45 @@

          +# NR2F2

          +

          +## History

          +Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2021-05-05 : Hübschmann : DLBCL

          +```

          +

          +## Relevance tier by entity

          +

          +|Entity|Tier|Description                              |

          +|:------:|:----:|-----------------------------------------|

          +|![DLBCL](images/icons/DLBCL_tier2.png) |2   |relevance in DLBCL not firmly established|

          +

          +## Mutation incidence in large patient cohorts (GAMBL reanalysis)

          +

          +|Entity|source        |frequency (%)|

          +|:------:|:--------------:|:-------------:|

          +|DLBCL |GAMBL genomes |NA           |

          +|DLBCL |Schmitz cohort|NA           |

          +|DLBCL |Reddy cohort  |NA           |

          +|DLBCL |Chapuy cohort |NA           |

          +

          +View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein_hg38.html)

          +

          +View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_hg38.html)

          +

          +![](images/proteinpaint/N2RF2.svg)

          +

          +## All Mutations

          +

          +[SP192856](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP192856.html)

          +[SP193004](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193004.html)

          +[SP193967](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193967.html)

          +

          +## References

          +1.  Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491

          +

          +

          +<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->

          +<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->

				papers/hubschmannMutationalMechanismsShaping2021b.md
			
          @@ -63,7 +63,7 @@ All other DLBCL studies, DLBCL Tier 2, 175

           |[LRP12](../LRP12)| |2 |&starf; &starf; &starf; &star; &star;|**Pass**|

           |[MGEA5](../MGEA5)|2 | |&starf; &starf; &starf; &star; &star;|**Pass**|

           |[MYCBP2](../MYCBP2)|2 | |&starf; &starf; &starf; &starf; &star;|**Pass**|

          -|[N2RF2](../N2RF2)| |2 |||

          +|[NR2F2](../N2RF2)| |2 |||

           |[PDS5B](../PDS5B)|2 |2 |||

           |[PNPO](../PNPO)| |2 |||

           |[PPP4C](../PPP4C)|2 | |||

...	...	@@ -260,7 +260,7 @@ link-citations: true
260	260	\|[MYBPC2](MYBPC2)\|2\|[@schmitzGeneticsPathogenesisDiffuse2018a]\|\|
261	261	\|[MYO1E](MYO1E)\|2, aSHM\|\|\|
262	262	\|[MYOM2](MYOM2)\|2\|[@pasqualucciAnalysisCodingGenome2011]\|\|
263		-\|[N2RF2](N2RF2)\|2\|[@hubschmannMutationalMechanismsShaping2021b]\|\|
	263	+\|[NR2F2](N2RF2)\|2\|[@hubschmannMutationalMechanismsShaping2021b]\|\|
264	264	\|[NANOG](NANOG)\|2\|[@chapuyMolecularSubtypesDiffuse2018b]\|\|
265	265	\|[NAV1](NAV1)\|2\|[@chapuyMolecularSubtypesDiffuse2018b]\|\|
266	266	\|[NCOA3](NCOA3)\|2, aSHM\|\|\|

...	...	@@ -1,43 +0,0 @@
1		-# N2RF2
2		-
3		-## History
4		-Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
5		-
6		-```mermaid
7		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8		-timeline
9		- title Publication timing
10		- 2021-05-05 : Hübschmann : DLBCL
11		-```
12		-
13		-## Relevance tier by entity
14		-
15		-\|Entity\|Tier\|Description \|
16		-\|:------:\|:----:\|-----------------------------------------\|
17		-\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
18		-
19		-## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20		-
21		-\|Entity\|source \|frequency (%)\|
22		-\|:------:\|:--------------:\|:-------------:\|
23		-\|DLBCL \|GAMBL genomes \|NA \|
24		-\|DLBCL \|Schmitz cohort\|NA \|
25		-\|DLBCL \|Reddy cohort \|NA \|
26		-\|DLBCL \|Chapuy cohort \|NA \|
27		-
28		-View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein_hg38.html)
29		-
30		-View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_hg38.html)
31		-
32		-![](images/proteinpaint/N2RF2.svg)
33		-
34		-## N2RF2 Expression
35		-![](images/gene_expression/N2RF2_by_pathology.svg)
36		-
37		-
38		-## References
39		-1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
40		-
41		-
42		-<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
43		-<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->

...	...	@@ -0,0 +1,45 @@
	1	+# NR2F2
	2	+
	3	+## History
	4	+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
	5	+
	6	+```mermaid
	7	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	8	+timeline
	9	+ title Publication timing
	10	+ 2021-05-05 : Hübschmann : DLBCL
	11	+```
	12	+
	13	+## Relevance tier by entity
	14	+
	15	+\|Entity\|Tier\|Description \|
	16	+\|:------:\|:----:\|-----------------------------------------\|
	17	+\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
	18	+
	19	+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
	20	+
	21	+\|Entity\|source \|frequency (%)\|
	22	+\|:------:\|:--------------:\|:-------------:\|
	23	+\|DLBCL \|GAMBL genomes \|NA \|
	24	+\|DLBCL \|Schmitz cohort\|NA \|
	25	+\|DLBCL \|Reddy cohort \|NA \|
	26	+\|DLBCL \|Chapuy cohort \|NA \|
	27	+
	28	+View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_protein_hg38.html)
	29	+
	30	+View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N2RF2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/N2RF2_hg38.html)
	31	+
	32	+![](images/proteinpaint/N2RF2.svg)
	33	+
	34	+## All Mutations
	35	+
	36	+[SP192856](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP192856.html)
	37	+[SP193004](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193004.html)
	38	+[SP193967](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193967.html)
	39	+
	40	+## References
	41	+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
	42	+
	43	+
	44	+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
	45	+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->

...	...	@@ -63,7 +63,7 @@ All other DLBCL studies, DLBCL Tier 2, 175
63	63	\|[LRP12](../LRP12)\| \|2 \|&starf; &starf; &starf; &star; &star;\|Pass\|
64	64	\|[MGEA5](../MGEA5)\|2 \| \|&starf; &starf; &starf; &star; &star;\|Pass\|
65	65	\|[MYCBP2](../MYCBP2)\|2 \| \|&starf; &starf; &starf; &starf; &star;\|Pass\|
66		-\|[N2RF2](../N2RF2)\| \|2 \|\|\|
	66	+\|[NR2F2](../N2RF2)\| \|2 \|\|\|
67	67	\|[PDS5B](../PDS5B)\|2 \|2 \|\|\|
68	68	\|[PNPO](../PNPO)\| \|2 \|\|\|
69	69	\|[PPP4C](../PPP4C)\|2 \| \|\|\|