Changes in 0e57899: fix refs

				DLBCL_genes.md
			
          @@ -85,14 +85,14 @@ link-citations: true

           |[KRAS](KRAS)|1|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)[@lohrDiscoveryPrioritizationSomatic2012a]||

           |[LCOR](LCOR)|1|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)[@arthurGenomewideDiscoverySomatic2018]||

           |[LTB](LTB)|1|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)[@chapuyMolecularSubtypesDiffuse2018b]|[@paneaWholeGenomeLandscape2019; @deschGenotypingCirculatingTumor2020]|

          -|[MEF2B](MEF2B)|1|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@beaLandscapeSomaticMutations2013]|

          +|[MEF2B](MEF2B)|1-EE|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]|[@beaLandscapeSomaticMutations2013]|

           |[MEF2C](MEF2C)|1|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)[@arthurGenomewideDiscoverySomatic2018]||

           |[MGA](MGA)|1|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)[@zhangGeneticHeterogeneityDiffuse2013]|[@jalladesExomeSequencingIdentifies2017]|

           |[MPEG1](MPEG1)|1|[Morin et al](papers/morinMutationalStructuralAnalysis2013)[@morinMutationalStructuralAnalysis2013]||

           |[MS4A1](MS4A1)|1|[Rushton et al](papers/rushtonGeneticEvolutionaryPatterns2020)[@rushtonGeneticEvolutionaryPatterns2020]|[@mottokIntegrativeGenomicAnalysis2019b]|

           |[MTOR](MTOR)|1|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)[@zhangGeneticHeterogeneityDiffuse2013]|[@paneaWholeGenomeLandscape2019]|

           |[MYC](MYC)|1|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001a)[@pasqualucciHypermutationMultipleProtooncogenes2001a]|[@dunsCharacterizationDLBCLPMBL2021b; @johnstonCmycHypermutationBurkitt1992; @jalladesExomeSequencingIdentifies2017]|

          -|[MYD88](MYD88)|1|[Ngo et al](papers/ngoOncogenicallyActiveMYD882011a)[@ngoOncogenicallyActiveMYD882011a]|[@yanBCRTLRSignaling2012a]|

          +|[MYD88](MYD88)|1-EE|[Ngo et al](papers/ngoOncogenicallyActiveMYD882011a)[@ngoOncogenicallyActiveMYD882011a]|[@yanBCRTLRSignaling2012a]|

           |[NFKBIA](NFKBIA)|1|[Lake et al](papers/lakeMutationsNFKBIAEncoding2009)[@lakeMutationsNFKBIAEncoding2009]|[@wienandGenomicAnalysesFlowsorted2019b; @russler-germainMutationsAssociatedProgression2023b]|

           |[NFKBIE](NFKBIE)|1|[Morin et al](papers/morinGeneticLandscapesRelapsed2016)[@morinGeneticLandscapesRelapsed2016]|[@mansouriFrequentNFKBIEDeletions2016; @pararajalingamCodingNoncodingDrivers2020]|

           |[NFKBIZ](NFKBIZ)|1|[Morin et al](papers/morinGeneticLandscapesRelapsed2016)[@morinGeneticLandscapesRelapsed2016]||

				HNRNPH1.md
			
          @@ -6,7 +6,10 @@ link-citations: true

           # HNRNPH1

           ## Overview

          -Non-coding mutations, including synonymous and intronic mutations,  are enriched at splicing signals in exon 4 of HNRNPH1. These result in deregulated splicing and increased expression of the hnRNP H1 protein. This overexpression is linked to enhanced cell proliferation and survival, contributing to the aggressive nature of MCL. <sup>1,2</sup> Although initially characterized in MCL, the same pattern of mutations appears in a small number of DLBCLs.

          +Non-coding mutations, including synonymous and intronic mutations,  are enriched at splicing signals in exon 4 of HNRNPH1. 

          +

          +## Experimental Evidence

          +The common HNRNPH1 mutations cause deregulated splicing and increased expression of the hnRNP H1 protein. This overexpression is linked to enhanced cell proliferation and survival, contributing to the aggressive nature of MCL.[@pararajalingamCodingNoncodingDrivers2020]  Although initially characterized in MCL, the same pattern of mutations appears in a small number of DLBCLs.

           ## History

           ```mermaid

          @@ -20,8 +23,8 @@ timeline

           |Entity|Tier|Description               |

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

          -|![DLBCL](images/icons/DLBCL_tier1.png) |1   |high-confidence DLBCL gene[@pararajalingamCodingNoncodingDrivers2020]|

          -|![MCL](images/icons/MCL_tier1.png)   |1   |high-confidence MCL gene  [@pararajalingamCodingNoncodingDrivers2020]|

          +|![DLBCL](images/icons/DLBCL_tier1.png) |2-EE   |high-confidence DLBCL gene[@pararajalingamCodingNoncodingDrivers2020]|

          +|![MCL](images/icons/MCL_tier1.png)   |1-EE   |high-confidence MCL gene  [@pararajalingamCodingNoncodingDrivers2020]|

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

				MCL_genes.md
			
          @@ -45,7 +45,7 @@ WGS/exome, Bea 2013, 27

           |[ATM](ATM)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@reddyGeneticFunctionalDrivers2017; @braggioGenomicAnalysisMarginal2012]|

           |[BIRC3](BIRC3)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@dunsCharacterizationDLBCLPMBL2021b; @rossiAlterationBIRC3Multiple2011a; @arthurGenomewideDiscoverySomatic2018]|

           |[CARD11](CARD11)|1|[Wu et al](papers/wuGeneticHeterogeneityPrimary2016)[@wuGeneticHeterogeneityPrimary2016]|[@paneaWholeGenomeLandscape2019; @yanBCRTLRSignaling2012a; @lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011]|

          -|[CCND1](CCND1)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||

          +|[CCND1](CCND1)|1-EE|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]||

           |[DAZAP1](DAZAP1)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]||

           |[EWSR1](EWSR1)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]||

           |[HNRNPH1](HNRNPH1)|1-EE|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]||

          @@ -63,7 +63,7 @@ WGS/exome, Bea 2013, 27

           |[SYNE1](SYNE1)|1|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]||

           |[TERT](TERT)|1|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]||

           |[TLR2](TLR2)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@chapuyMolecularSubtypesDiffuse2018b]|

          -|[TP53](TP53)|1|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@tiacciPervasiveMutationsJAKSTAT2018b; @lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011; @wildaInactivationARFMDM2p53Pathway2004]|

          +|[TP53](TP53)|1-EE|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]|[@tiacciPervasiveMutationsJAKSTAT2018b; @lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011; @wildaInactivationARFMDM2p53Pathway2004]|

           |[UBR5](UBR5)|1|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]|[@zhangGeneticHeterogeneityDiffuse2013]|

           ## Tier 2 MCL genes

				MEF2B.md
			
          @@ -6,7 +6,10 @@ link-citations: true

           # MEF2B

           ## Overview

          -MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. MEF2B mutations are observed in a significant subset of follicular lymphoma cases, as well as in other B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL) and MCL.<sup>1</sup> MEF2B has known hotspot mutations that affect multiple distinct domains of the protein. 

          +MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. MEF2B mutations are observed in a significant subset of follicular lymphoma cases, as well as in other B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL) and MCL.[@morinFrequentMutationHistonemodifying2011; @beaLandscapeSomaticMutations2013] MEF2B has known hotspot mutations that affect multiple distinct domains of the protein. 

          +

          +## Experimental Evidence

          +Thus far, there is limited information about the consequence of MEF2B mutations in DLBCL, FL or MCL. One study showed that MEF2B mutations lead to deregulation of BCL6 expression.[@yingMEF2BMutationsLead]

           ## History

           ```mermaid

...	...	@@ -45,7 +45,7 @@ WGS/exome, Bea 2013, 27
45	45	\|[ATM](ATM)\|1\|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]\|[@reddyGeneticFunctionalDrivers2017; @braggioGenomicAnalysisMarginal2012]\|
46	46	\|[BIRC3](BIRC3)\|1\|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]\|[@dunsCharacterizationDLBCLPMBL2021b; @rossiAlterationBIRC3Multiple2011a; @arthurGenomewideDiscoverySomatic2018]\|
47	47	\|[CARD11](CARD11)\|1\|[Wu et al](papers/wuGeneticHeterogeneityPrimary2016)[@wuGeneticHeterogeneityPrimary2016]\|[@paneaWholeGenomeLandscape2019; @yanBCRTLRSignaling2012a; @lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011]\|
48		-\|[CCND1](CCND1)\|1\|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]\|\|
	48	+\|[CCND1](CCND1)\|1-EE\|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]\|\|
49	49	\|[DAZAP1](DAZAP1)\|1\|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]\|\|
50	50	\|[EWSR1](EWSR1)\|1\|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]\|\|
51	51	\|[HNRNPH1](HNRNPH1)\|1-EE\|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]\|\|
...	...	@@ -63,7 +63,7 @@ WGS/exome, Bea 2013, 27
63	63	\|[SYNE1](SYNE1)\|1\|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]\|\|
64	64	\|[TERT](TERT)\|1\|[Nadeu et al](papers/nadeuGenomicEpigenomicInsights2020b)[@nadeuGenomicEpigenomicInsights2020b]\|\|
65	65	\|[TLR2](TLR2)\|1\|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]\|[@chapuyMolecularSubtypesDiffuse2018b]\|
66		-\|[TP53](TP53)\|1\|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]\|[@tiacciPervasiveMutationsJAKSTAT2018b; @lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011; @wildaInactivationARFMDM2p53Pathway2004]\|
	66	+\|[TP53](TP53)\|1-EE\|[Bea et al](papers/beaLandscapeSomaticMutations2013)[@beaLandscapeSomaticMutations2013]\|[@tiacciPervasiveMutationsJAKSTAT2018b; @lohrDiscoveryPrioritizationSomatic2012a; @rossiCodingGenomeSplenic2012c; @morinFrequentMutationHistonemodifying2011; @wildaInactivationARFMDM2p53Pathway2004]\|
67	67	\|[UBR5](UBR5)\|1\|[Pararajalingam et al](papers/pararajalingamCodingNoncodingDrivers2020)[@pararajalingamCodingNoncodingDrivers2020]\|[@zhangGeneticHeterogeneityDiffuse2013]\|
68	68
69	69	## Tier 2 MCL genes

...	...	@@ -85,14 +85,14 @@ link-citations: true
85	85	\|[KRAS](KRAS)\|1\|[Lohr et al](papers/lohrDiscoveryPrioritizationSomatic2012a)[@lohrDiscoveryPrioritizationSomatic2012a]\|\|
86	86	\|[LCOR](LCOR)\|1\|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)[@arthurGenomewideDiscoverySomatic2018]\|\|
87	87	\|[LTB](LTB)\|1\|[Chapuy et al](papers/chapuyMolecularSubtypesDiffuse2018b)[@chapuyMolecularSubtypesDiffuse2018b]\|[@paneaWholeGenomeLandscape2019; @deschGenotypingCirculatingTumor2020]\|
88		-\|[MEF2B](MEF2B)\|1\|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]\|[@beaLandscapeSomaticMutations2013]\|
	88	+\|[MEF2B](MEF2B)\|1-EE\|[Morin et al](papers/morinFrequentMutationHistonemodifying2011)[@morinFrequentMutationHistonemodifying2011]\|[@beaLandscapeSomaticMutations2013]\|
89	89	\|[MEF2C](MEF2C)\|1\|[Arthur et al](papers/arthurGenomewideDiscoverySomatic2018)[@arthurGenomewideDiscoverySomatic2018]\|\|
90	90	\|[MGA](MGA)\|1\|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)[@zhangGeneticHeterogeneityDiffuse2013]\|[@jalladesExomeSequencingIdentifies2017]\|
91	91	\|[MPEG1](MPEG1)\|1\|[Morin et al](papers/morinMutationalStructuralAnalysis2013)[@morinMutationalStructuralAnalysis2013]\|\|
92	92	\|[MS4A1](MS4A1)\|1\|[Rushton et al](papers/rushtonGeneticEvolutionaryPatterns2020)[@rushtonGeneticEvolutionaryPatterns2020]\|[@mottokIntegrativeGenomicAnalysis2019b]\|
93	93	\|[MTOR](MTOR)\|1\|[Zhang et al](papers/zhangGeneticHeterogeneityDiffuse2013)[@zhangGeneticHeterogeneityDiffuse2013]\|[@paneaWholeGenomeLandscape2019]\|
94	94	\|[MYC](MYC)\|1\|[Pasqualucci et al](papers/pasqualucciHypermutationMultipleProtooncogenes2001a)[@pasqualucciHypermutationMultipleProtooncogenes2001a]\|[@dunsCharacterizationDLBCLPMBL2021b; @johnstonCmycHypermutationBurkitt1992; @jalladesExomeSequencingIdentifies2017]\|
95		-\|[MYD88](MYD88)\|1\|[Ngo et al](papers/ngoOncogenicallyActiveMYD882011a)[@ngoOncogenicallyActiveMYD882011a]\|[@yanBCRTLRSignaling2012a]\|
	95	+\|[MYD88](MYD88)\|1-EE\|[Ngo et al](papers/ngoOncogenicallyActiveMYD882011a)[@ngoOncogenicallyActiveMYD882011a]\|[@yanBCRTLRSignaling2012a]\|
96	96	\|[NFKBIA](NFKBIA)\|1\|[Lake et al](papers/lakeMutationsNFKBIAEncoding2009)[@lakeMutationsNFKBIAEncoding2009]\|[@wienandGenomicAnalysesFlowsorted2019b; @russler-germainMutationsAssociatedProgression2023b]\|
97	97	\|[NFKBIE](NFKBIE)\|1\|[Morin et al](papers/morinGeneticLandscapesRelapsed2016)[@morinGeneticLandscapesRelapsed2016]\|[@mansouriFrequentNFKBIEDeletions2016; @pararajalingamCodingNoncodingDrivers2020]\|
98	98	\|[NFKBIZ](NFKBIZ)\|1\|[Morin et al](papers/morinGeneticLandscapesRelapsed2016)[@morinGeneticLandscapesRelapsed2016]\|\|

...	...	@@ -6,7 +6,10 @@ link-citations: true
6	6	# HNRNPH1
7	7
8	8	## Overview
9		-Non-coding mutations, including synonymous and intronic mutations, are enriched at splicing signals in exon 4 of HNRNPH1. These result in deregulated splicing and increased expression of the hnRNP H1 protein. This overexpression is linked to enhanced cell proliferation and survival, contributing to the aggressive nature of MCL. <sup>1,2</sup> Although initially characterized in MCL, the same pattern of mutations appears in a small number of DLBCLs.
	9	+Non-coding mutations, including synonymous and intronic mutations, are enriched at splicing signals in exon 4 of HNRNPH1.
	10	+
	11	+## Experimental Evidence
	12	+The common HNRNPH1 mutations cause deregulated splicing and increased expression of the hnRNP H1 protein. This overexpression is linked to enhanced cell proliferation and survival, contributing to the aggressive nature of MCL.[@pararajalingamCodingNoncodingDrivers2020] Although initially characterized in MCL, the same pattern of mutations appears in a small number of DLBCLs.
10	13
11	14	## History
12	15	```mermaid
...	...	@@ -20,8 +23,8 @@ timeline
20	23
21	24	\|Entity\|Tier\|Description \|
22	25	\|:------:\|:----:\|--------------------------\|
23		-\|![DLBCL](images/icons/DLBCL_tier1.png) \|1 \|high-confidence DLBCL gene[@pararajalingamCodingNoncodingDrivers2020]\|
24		-\|![MCL](images/icons/MCL_tier1.png) \|1 \|high-confidence MCL gene [@pararajalingamCodingNoncodingDrivers2020]\|
	26	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|2-EE \|high-confidence DLBCL gene[@pararajalingamCodingNoncodingDrivers2020]\|
	27	+\|![MCL](images/icons/MCL_tier1.png) \|1-EE \|high-confidence MCL gene [@pararajalingamCodingNoncodingDrivers2020]\|
25	28
26	29	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27	30

...	...	@@ -6,7 +6,10 @@ link-citations: true
6	6	# MEF2B
7	7
8	8	## Overview
9		-MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. MEF2B mutations are observed in a significant subset of follicular lymphoma cases, as well as in other B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL) and MCL.<sup>1</sup> MEF2B has known hotspot mutations that affect multiple distinct domains of the protein.
	9	+MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. MEF2B mutations are observed in a significant subset of follicular lymphoma cases, as well as in other B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL) and MCL.[@morinFrequentMutationHistonemodifying2011; @beaLandscapeSomaticMutations2013] MEF2B has known hotspot mutations that affect multiple distinct domains of the protein.
	10	+
	11	+## Experimental Evidence
	12	+Thus far, there is limited information about the consequence of MEF2B mutations in DLBCL, FL or MCL. One study showed that MEF2B mutations lead to deregulation of BCL6 expression.[@yingMEF2BMutationsLead]
10	13
11	14	## History
12	15	```mermaid