Changes in 3a6ed6a: update

				MZL_genes.md
			
          @@ -5,7 +5,9 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -## Origins of MZL genes

          +[[_TOC_]]

          +

          +## MZL genes

           ![](images/MZL_sankey1-1.svg)

          @@ -13,51 +15,6 @@ link-citations: true

           [[include:pages/MZL_Tier1]]

          -

          -|Gene|Summary| First MZL study | Other entities | QC result |

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

          -|[ACTB](ACTB)|MZL Tier 1||[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012; @wienandGenomicAnalysesFlowsorted2019]||

          -|[ARID1A](ARID1A)|MZL Tier 1|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@krysiakRecurrentSomaticMutations2017; @loveGeneticLandscapeMutations2012; @wienandGenomicAnalysesFlowsorted2019; @zhangGeneticHeterogeneityDiffuse2013]||

          -|[ATM](ATM)|MZL Tier 1 |[Braggio et al](papers/braggioGenomicAnalysisMarginal2012)|[@beaLandscapeSomaticMutations2013; @reddyGeneticFunctionalDrivers2017]||

          -|[BCL10](BCL10)|MZL Tier 1 |[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@morinFrequentMutationHistonemodifying2011; @russler-germainMutationsAssociatedProgression2023]||

          -|[BCL7A](BCL7A)|MZL Tier 1 ||[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]||

          -|[BIRC3](BIRC3)|MZL Tier 1 |[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@arthurGenomewideDiscoverySomatic2018; @beaLandscapeSomaticMutations2013; @dunsCharacterizationDLBCLPMBL2021]||

          -|[BRAF](BRAF)|MZL Tier 1 ||[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011]||

          -|[BTG1](BTG1)|MZL Tier 1 ||[@burkhardtClinicalRelevanceMolecular2022; @drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021]||

          -|[CARD11](CARD11)|MZL Tier 1 |[Yan et al](papers/yanBCRTLRSignaling2012)|[@lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016]||

          -|[CCND3](CCND3)|MZL Tier 1|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011; @richterRecurrentMutationID32012]||

          -|[CXCR4](CXCR4)|MZL Tier 1 ||[@khodabakhshiRecurrentTargetsAberrant2012; @krysiakRecurrentSomaticMutations2017; @paneaWholeGenomeLandscape2019]||

          -|[DTX1](DTX1)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @zhangGeneticHeterogeneityDiffuse2013]||

          -|[EP300](EP300)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@pasqualucciInactivatingMutationsAcetyltransferase2011]||

          -|[EZH2](EZH2)|MZL Tier 1 ||[@loveGeneticLandscapeMutations2012; @morinSomaticMutationsAltering2010; @mottokIntegrativeGenomicAnalysis2019]||

          -|[FAS](FAS)|MZL Tier 1 |[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@morinFrequentMutationHistonemodifying2011; @schollMutationsRegionFAS2007]||

          -|[FAT1](FAT1)|MZL Tier 1 |[Spina et al](papers/spinaGeneticsNodalMarginal2016)|||

          -|[FOXO1](FOXO1)|MZL Tier 1 ||[@dunsCharacterizationDLBCLPMBL2021; @morinFrequentMutationHistonemodifying2011; @schmitzBurkittLymphomaPathogenesis2012]||

          -|[ID3](ID3)|MZL Tier 1 |[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@richterRecurrentMutationID32012; @schmitzGeneticsPathogenesisDiffuse2018]||

          -|[KLF2](KLF2)|MZL Tier 1 |[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)|[@deschGenotypingCirculatingTumor2020; @drevalGeneticSubdivisionsFollicular2023; @pasqualucciAnalysisCodingGenome2011]||

          -|[KLHL6](KLHL6)|MZL Tier 1 |[Ganapathi et al](papers/ganapathiGeneticLandscapeDural2016)|[@morinFrequentMutationHistonemodifying2011]||

          -|[KMT2D](KMT2D)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011]||

          -|[MAP3K14](MAP3K14)|MZL Tier 1|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@ottoGeneticLesionsTRAF32012]||

          -|[MPEG1](MPEG1)|MZL Tier 1 ||[@morinMutationalStructuralAnalysis2013]||

          -|[MYD88](MYD88)|MZL Tier 1|[Yan et al](papers/yanBCRTLRSignaling2012)|[@drevalGeneticSubdivisionsFollicular2023; @ngoOncogenicallyActiveMYD882011]||

          -|[NCOR2](NCOR2)|MZL Tier 1|[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@sarkozyMutationalLandscapeGray2021; @schmitzBurkittLymphomaPathogenesis2012]||

          -|[NOL9](NOL9)|MZL Tier 1 |[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@schmitzGeneticsPathogenesisDiffuse2018]||

          -|[NOTCH1](NOTCH1)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @loveGeneticLandscapeMutations2012; @pasqualucciAnalysisCodingGenome2011]||

          -|[NOTCH2](NOTCH2)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @zhangGeneticHeterogeneityDiffuse2013]||

          -|[PCLO](PCLO)|MZL Tier 1 ||[@lohrDiscoveryPrioritizationSomatic2012]||

          -|[POU2AF1](POU2AF1)|MZL Tier 1||[@chapuyMolecularSubtypesDiffuse2018; @krysiakRecurrentSomaticMutations2017]||

          -|[PTPRD](PTPRD)|MZL Tier 1 |[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@drevalGeneticSubdivisionsFollicular2023]||

          -|[SIN3A](SIN3A)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@chapuyMolecularSubtypesDiffuse2018; @grandeGenomewideDiscoverySomatic2019]||

          -|[SOCS1](SOCS1)|MZL Tier 1 ||[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006]||

          -|[SPEN](SPEN)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@albuquerqueEnhancingKnowledgeDiscovery2017; @sarkozyMutationalLandscapeGray2021]||

          -|[STAT6](STAT6)|MZL Tier 1 ||Ritz et al||

          -|[TBL1XR1](TBL1XR1)|MZL Tier 1|[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012]||

          -|[TNFAIP3](TNFAIP3)|MZL Tier 1 |[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@compagnoMutationsMultipleGenes2009; @drevalGeneticSubdivisionsFollicular2023; @schmitzTNFAIP3A20Tumor2009]||

          -|[TNFRSF14](TNFRSF14)|MZL Tier 1 |[Spina et al](papers/spinaGeneticsNodalMarginal2016)|[@cheungAcquiredTNFRSF14Mutations2010; @morinFrequentMutationHistonemodifying2011]||

          -|[TP53](TP53)|MZL Tier 1 |[Rossi et al](papers/rossiCodingGenomeSplenic2012)|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]||

          -|[TRAF3](TRAF3)|MZL Tier 1 |[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)|[@ottoGeneticLesionsTRAF32012; @pasqualucciAnalysisCodingGenome2011]||

          -

          -

           ## Tier 2, low-confidence MZL genes

           [[include:pages/MZL_Tier2]]

...	...	@@ -5,7 +5,9 @@ csl: 'NLM.csl'
5	5	link-citations: true
6	6	---
7	7
8		-## Origins of MZL genes
	8	+[[_TOC_]]
	9	+
	10	+## MZL genes
9	11
10	12	![](images/MZL_sankey1-1.svg)
11	13
...	...	@@ -13,51 +15,6 @@ link-citations: true
13	15
14	16	[[include:pages/MZL_Tier1]]
15	17
16		-
17		-\|Gene\|Summary\| First MZL study \| Other entities \| QC result \|
18		-\|:-:\|:--:\|:-:\|:-\|:-\|
19		-\|[ACTB](ACTB)\|MZL Tier 1\|\|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012; @wienandGenomicAnalysesFlowsorted2019]\|\|
20		-\|[ARID1A](ARID1A)\|MZL Tier 1\|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@krysiakRecurrentSomaticMutations2017; @loveGeneticLandscapeMutations2012; @wienandGenomicAnalysesFlowsorted2019; @zhangGeneticHeterogeneityDiffuse2013]\|\|
21		-\|[ATM](ATM)\|MZL Tier 1 \|[Braggio et al](papers/braggioGenomicAnalysisMarginal2012)\|[@beaLandscapeSomaticMutations2013; @reddyGeneticFunctionalDrivers2017]\|\|
22		-\|[BCL10](BCL10)\|MZL Tier 1 \|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|[@morinFrequentMutationHistonemodifying2011; @russler-germainMutationsAssociatedProgression2023]\|\|
23		-\|[BCL7A](BCL7A)\|MZL Tier 1 \|\|[@grandeGenomewideDiscoverySomatic2019; @krysiakRecurrentSomaticMutations2017; @morinFrequentMutationHistonemodifying2011; @reichelFlowSortingExome2015]\|\|
24		-\|[BIRC3](BIRC3)\|MZL Tier 1 \|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)\|[@arthurGenomewideDiscoverySomatic2018; @beaLandscapeSomaticMutations2013; @dunsCharacterizationDLBCLPMBL2021]\|\|
25		-\|[BRAF](BRAF)\|MZL Tier 1 \|\|[@loveGeneticLandscapeMutations2012; @tiacciBRAFMutationsHairycell2011]\|\|
26		-\|[BTG1](BTG1)\|MZL Tier 1 \|\|[@burkhardtClinicalRelevanceMolecular2022; @drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @sarkozyMutationalLandscapeGray2021]\|\|
27		-\|[CARD11](CARD11)\|MZL Tier 1 \|[Yan et al](papers/yanBCRTLRSignaling2012)\|[@lenzOncogenicCARD11Mutations2008; @morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016]\|\|
28		-\|[CCND3](CCND3)\|MZL Tier 1\|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)\|[@deschGenotypingCirculatingTumor2020; @morinFrequentMutationHistonemodifying2011; @richterRecurrentMutationID32012]\|\|
29		-\|[CXCR4](CXCR4)\|MZL Tier 1 \|\|[@khodabakhshiRecurrentTargetsAberrant2012; @krysiakRecurrentSomaticMutations2017; @paneaWholeGenomeLandscape2019]\|\|
30		-\|[DTX1](DTX1)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@gomezUltraDeepSequencingReveals2023; @loveGeneticLandscapeMutations2012; @zhangGeneticHeterogeneityDiffuse2013]\|\|
31		-\|[EP300](EP300)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@pasqualucciInactivatingMutationsAcetyltransferase2011]\|\|
32		-\|[EZH2](EZH2)\|MZL Tier 1 \|\|[@loveGeneticLandscapeMutations2012; @morinSomaticMutationsAltering2010; @mottokIntegrativeGenomicAnalysis2019]\|\|
33		-\|[FAS](FAS)\|MZL Tier 1 \|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|[@morinFrequentMutationHistonemodifying2011; @schollMutationsRegionFAS2007]\|\|
34		-\|[FAT1](FAT1)\|MZL Tier 1 \|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|\|\|
35		-\|[FOXO1](FOXO1)\|MZL Tier 1 \|\|[@dunsCharacterizationDLBCLPMBL2021; @morinFrequentMutationHistonemodifying2011; @schmitzBurkittLymphomaPathogenesis2012]\|\|
36		-\|[ID3](ID3)\|MZL Tier 1 \|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|[@richterRecurrentMutationID32012; @schmitzGeneticsPathogenesisDiffuse2018]\|\|
37		-\|[KLF2](KLF2)\|MZL Tier 1 \|[Jallades et al](papers/jalladesExomeSequencingIdentifies2017)\|[@deschGenotypingCirculatingTumor2020; @drevalGeneticSubdivisionsFollicular2023; @pasqualucciAnalysisCodingGenome2011]\|\|
38		-\|[KLHL6](KLHL6)\|MZL Tier 1 \|[Ganapathi et al](papers/ganapathiGeneticLandscapeDural2016)\|[@morinFrequentMutationHistonemodifying2011]\|\|
39		-\|[KMT2D](KMT2D)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@beaLandscapeSomaticMutations2013; @deschGenotypingCirculatingTumor2020; @grandeGenomewideDiscoverySomatic2019; @morinFrequentMutationHistonemodifying2011]\|\|
40		-\|[MAP3K14](MAP3K14)\|MZL Tier 1\|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@ottoGeneticLesionsTRAF32012]\|\|
41		-\|[MPEG1](MPEG1)\|MZL Tier 1 \|\|[@morinMutationalStructuralAnalysis2013]\|\|
42		-\|[MYD88](MYD88)\|MZL Tier 1\|[Yan et al](papers/yanBCRTLRSignaling2012)\|[@drevalGeneticSubdivisionsFollicular2023; @ngoOncogenicallyActiveMYD882011]\|\|
43		-\|[NCOR2](NCOR2)\|MZL Tier 1\|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|[@sarkozyMutationalLandscapeGray2021; @schmitzBurkittLymphomaPathogenesis2012]\|\|
44		-\|[NOL9](NOL9)\|MZL Tier 1 \|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|[@schmitzGeneticsPathogenesisDiffuse2018]\|\|
45		-\|[NOTCH1](NOTCH1)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@beaLandscapeSomaticMutations2013; @loveGeneticLandscapeMutations2012; @pasqualucciAnalysisCodingGenome2011]\|\|
46		-\|[NOTCH2](NOTCH2)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@beaLandscapeSomaticMutations2013; @zhangGeneticHeterogeneityDiffuse2013]\|\|
47		-\|[PCLO](PCLO)\|MZL Tier 1 \|\|[@lohrDiscoveryPrioritizationSomatic2012]\|\|
48		-\|[POU2AF1](POU2AF1)\|MZL Tier 1\|\|[@chapuyMolecularSubtypesDiffuse2018; @krysiakRecurrentSomaticMutations2017]\|\|
49		-\|[PTPRD](PTPRD)\|MZL Tier 1 \|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|[@drevalGeneticSubdivisionsFollicular2023]\|\|
50		-\|[SIN3A](SIN3A)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@chapuyMolecularSubtypesDiffuse2018; @grandeGenomewideDiscoverySomatic2019]\|\|
51		-\|[SOCS1](SOCS1)\|MZL Tier 1 \|\|[@drevalGeneticSubdivisionsFollicular2023; @morinFrequentMutationHistonemodifying2011; @wenigerMutationsTumorSuppressor2006]\|\|
52		-\|[SPEN](SPEN)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@albuquerqueEnhancingKnowledgeDiscovery2017; @sarkozyMutationalLandscapeGray2021]\|\|
53		-\|[STAT6](STAT6)\|MZL Tier 1 \|\|Ritz et al\|\|
54		-\|[TBL1XR1](TBL1XR1)\|MZL Tier 1\|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@drevalGeneticSubdivisionsFollicular2023; @lohrDiscoveryPrioritizationSomatic2012]\|\|
55		-\|[TNFAIP3](TNFAIP3)\|MZL Tier 1 \|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)\|[@compagnoMutationsMultipleGenes2009; @drevalGeneticSubdivisionsFollicular2023; @schmitzTNFAIP3A20Tumor2009]\|\|
56		-\|[TNFRSF14](TNFRSF14)\|MZL Tier 1 \|[Spina et al](papers/spinaGeneticsNodalMarginal2016)\|[@cheungAcquiredTNFRSF14Mutations2010; @morinFrequentMutationHistonemodifying2011]\|\|
57		-\|[TP53](TP53)\|MZL Tier 1 \|[Rossi et al](papers/rossiCodingGenomeSplenic2012)\|[@beaLandscapeSomaticMutations2013; @morinFrequentMutationHistonemodifying2011; @tiacciPervasiveMutationsJAKSTAT2018; @wildaInactivationARFMDM2p53Pathway2004]\|\|
58		-\|[TRAF3](TRAF3)\|MZL Tier 1 \|[Rossi et al](papers/rossiAlterationBIRC3Multiple2011)\|[@ottoGeneticLesionsTRAF32012; @pasqualucciAnalysisCodingGenome2011]\|\|
59		-
60		-
61	18	## Tier 2, low-confidence MZL genes
62	19
63	20	[[include:pages/MZL_Tier2]]