Changes in 7ce9b77: modify figure lable

				Supplemental_Methods_and_Results.md
			
          @@ -8,7 +8,7 @@ csl: NLM.csl

           ## Sources of B-cell lymphoma genes

          -Any study that described at least one gene as recurrently mutated in DLBCL, FL or BL was eligible to contribute to the gene lists. This included 37 studies for DLBCL,[@albuquerqueEnhancingKnowledgeDiscovery2017; @arthurGenomewideDiscoverySomatic2018; @bohleRoleEarlyBcell2013; @chapuyMolecularSubtypesDiffuse2018; @compagnoMutationsMultipleGenes2009; @davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021; @fanComprehensiveCharacterizationDriver2020; @hubschmannMutationalMechanismsShaping2021; @khodabakhshiRecurrentTargetsAberrant2012; @kwanhianMicroRNA142Mutated202012; @lenzOncogenicCARD11Mutations2008; @lohrDiscoveryPrioritizationSomatic2012; @mareschalWholeExomeSequencing2016; @morinFrequentMutationHistonemodifying2011; @morinGeneticLandscapesRelapsed2016; @morinMutationalStructuralAnalysis2013; @morinSomaticMutationsAltering2010; @ngoOncogenicallyActiveMYD882011; @novakWholeexomeAnalysisReveals2015; @okosunRecurrentMTORC1activatingRRAGC2016; @pararajalingamCodingNoncodingDrivers2020; @pasqualucciAnalysisCodingGenome2011; @pasqualucciHypermutationMultipleProtooncogenes2001; @pasqualucciInactivatingMutationsAcetyltransferase2011; @pasqualucciInactivationPRDM1BLIMP12006; @reddyGeneticFunctionalDrivers2017; @rushtonGeneticEvolutionaryPatterns2020; @schmitzGeneticsPathogenesisDiffuse2018; @schollMutationsRegionFAS2007; @shinBRAFV600EMAP2K12015; @tanakaFrequentIncidenceSomatic1992; @thomasMutationalAnalysisIkappaBalpha2004; @tiacciBRAFMutationsHairycell2011; @yildizActivatingSTAT6Mutations2015; @zhangGeneticHeterogeneityDiffuse2013]

          +Any study that described at least one gene as recurrently mutated in DLBCL, FL or BL was eligible to contribute to the gene lists. The current lists relied on a total of 37 studies for DLBCL,[@albuquerqueEnhancingKnowledgeDiscovery2017; @arthurGenomewideDiscoverySomatic2018; @bohleRoleEarlyBcell2013; @chapuyMolecularSubtypesDiffuse2018; @compagnoMutationsMultipleGenes2009; @davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021; @fanComprehensiveCharacterizationDriver2020; @hubschmannMutationalMechanismsShaping2021; @khodabakhshiRecurrentTargetsAberrant2012; @kwanhianMicroRNA142Mutated202012; @lenzOncogenicCARD11Mutations2008; @lohrDiscoveryPrioritizationSomatic2012; @mareschalWholeExomeSequencing2016; @morinFrequentMutationHistonemodifying2011; @morinGeneticLandscapesRelapsed2016; @morinMutationalStructuralAnalysis2013; @morinSomaticMutationsAltering2010; @ngoOncogenicallyActiveMYD882011; @novakWholeexomeAnalysisReveals2015; @okosunRecurrentMTORC1activatingRRAGC2016; @pararajalingamCodingNoncodingDrivers2020; @pasqualucciAnalysisCodingGenome2011; @pasqualucciHypermutationMultipleProtooncogenes2001; @pasqualucciInactivatingMutationsAcetyltransferase2011; @pasqualucciInactivationPRDM1BLIMP12006; @reddyGeneticFunctionalDrivers2017; @rushtonGeneticEvolutionaryPatterns2020; @schmitzGeneticsPathogenesisDiffuse2018; @schollMutationsRegionFAS2007; @shinBRAFV600EMAP2K12015; @tanakaFrequentIncidenceSomatic1992; @thomasMutationalAnalysisIkappaBalpha2004; @tiacciBRAFMutationsHairycell2011; @yildizActivatingSTAT6Mutations2015; @zhangGeneticHeterogeneityDiffuse2013]

           15 studies for FL,[@barariaCathepsinAlterationsInduce2020; @cheungAcquiredTNFRSF14Mutations2010; @drevalGeneticSubdivisionsFollicular2023; @hubschmannMutationalMechanismsShaping2021; @krysiakRecurrentSomaticMutations2017; @laurentFollicularLymphomaComprises2024; @louissaintPediatrictypeNodalFollicular2016; @maSubtypespecificCooccurringGenetic2022; @morinFrequentMutationHistonemodifying2011; @morinSomaticMutationsAltering2010; @okosunRecurrentMTORC1activatingRRAGC2016; @pasqualucciInactivatingMutationsAcetyltransferase2011; @rossiAberrantSomaticHypermutation2006; @russler-germainMutationsAssociatedProgression2023; @yildizActivatingSTAT6Mutations2015] and 13 studies for BL.[@abateDistinctViralMutational2015; @burkhardtClinicalRelevanceMolecular2022; @grandeGenomewideDiscoverySomatic2019; @johnstonCmycHypermutationBurkitt1992; @loveGeneticLandscapeMutations2012; @maSubtypespecificCooccurringGenetic2022; @muppidiLossSignalingGa132014; @paneaWholeGenomeLandscape2019; @richterRecurrentMutationID32012; @schmitzBurkittLymphomaPathogenesis2012; @thomasGeneticSubgroupsInform2023; @wildaInactivationARFMDM2p53Pathway2004; @zhouSporadicEndemicBurkitt2019]

           ## Procedure for gene retirement (Tier 3) 

          @@ -89,13 +89,13 @@ The FLAGS rank of DLBCL genes in Tier 1, 2 and 3 is compared. The genes in the C

           ### CARD4 - pass

          -![CARD4](primary/Love_CARD4.svg)

          +![](primary/Love_CARD4.svg)

           Average rating: &starf; &starf; &starf; &starf; &star;

           ### ACAD9 - fail (insufficient support) 

          -![ACAD9](primary/Love_ACAD9.svg)

          +![](primary/Love_ACAD9.svg)

           Average rating: &starf; &star; &star; &star; &star;

...	...	@@ -8,7 +8,7 @@ csl: NLM.csl
8	8
9	9	## Sources of B-cell lymphoma genes
10	10
11		-Any study that described at least one gene as recurrently mutated in DLBCL, FL or BL was eligible to contribute to the gene lists. This included 37 studies for DLBCL,[@albuquerqueEnhancingKnowledgeDiscovery2017; @arthurGenomewideDiscoverySomatic2018; @bohleRoleEarlyBcell2013; @chapuyMolecularSubtypesDiffuse2018; @compagnoMutationsMultipleGenes2009; @davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021; @fanComprehensiveCharacterizationDriver2020; @hubschmannMutationalMechanismsShaping2021; @khodabakhshiRecurrentTargetsAberrant2012; @kwanhianMicroRNA142Mutated202012; @lenzOncogenicCARD11Mutations2008; @lohrDiscoveryPrioritizationSomatic2012; @mareschalWholeExomeSequencing2016; @morinFrequentMutationHistonemodifying2011; @morinGeneticLandscapesRelapsed2016; @morinMutationalStructuralAnalysis2013; @morinSomaticMutationsAltering2010; @ngoOncogenicallyActiveMYD882011; @novakWholeexomeAnalysisReveals2015; @okosunRecurrentMTORC1activatingRRAGC2016; @pararajalingamCodingNoncodingDrivers2020; @pasqualucciAnalysisCodingGenome2011; @pasqualucciHypermutationMultipleProtooncogenes2001; @pasqualucciInactivatingMutationsAcetyltransferase2011; @pasqualucciInactivationPRDM1BLIMP12006; @reddyGeneticFunctionalDrivers2017; @rushtonGeneticEvolutionaryPatterns2020; @schmitzGeneticsPathogenesisDiffuse2018; @schollMutationsRegionFAS2007; @shinBRAFV600EMAP2K12015; @tanakaFrequentIncidenceSomatic1992; @thomasMutationalAnalysisIkappaBalpha2004; @tiacciBRAFMutationsHairycell2011; @yildizActivatingSTAT6Mutations2015; @zhangGeneticHeterogeneityDiffuse2013]
	11	+Any study that described at least one gene as recurrently mutated in DLBCL, FL or BL was eligible to contribute to the gene lists. The current lists relied on a total of 37 studies for DLBCL,[@albuquerqueEnhancingKnowledgeDiscovery2017; @arthurGenomewideDiscoverySomatic2018; @bohleRoleEarlyBcell2013; @chapuyMolecularSubtypesDiffuse2018; @compagnoMutationsMultipleGenes2009; @davisChronicActiveBcellreceptor2010; @drevalGeneticSubdivisionsFollicular2023; @dunsCharacterizationDLBCLPMBL2021; @fanComprehensiveCharacterizationDriver2020; @hubschmannMutationalMechanismsShaping2021; @khodabakhshiRecurrentTargetsAberrant2012; @kwanhianMicroRNA142Mutated202012; @lenzOncogenicCARD11Mutations2008; @lohrDiscoveryPrioritizationSomatic2012; @mareschalWholeExomeSequencing2016; @morinFrequentMutationHistonemodifying2011; @morinGeneticLandscapesRelapsed2016; @morinMutationalStructuralAnalysis2013; @morinSomaticMutationsAltering2010; @ngoOncogenicallyActiveMYD882011; @novakWholeexomeAnalysisReveals2015; @okosunRecurrentMTORC1activatingRRAGC2016; @pararajalingamCodingNoncodingDrivers2020; @pasqualucciAnalysisCodingGenome2011; @pasqualucciHypermutationMultipleProtooncogenes2001; @pasqualucciInactivatingMutationsAcetyltransferase2011; @pasqualucciInactivationPRDM1BLIMP12006; @reddyGeneticFunctionalDrivers2017; @rushtonGeneticEvolutionaryPatterns2020; @schmitzGeneticsPathogenesisDiffuse2018; @schollMutationsRegionFAS2007; @shinBRAFV600EMAP2K12015; @tanakaFrequentIncidenceSomatic1992; @thomasMutationalAnalysisIkappaBalpha2004; @tiacciBRAFMutationsHairycell2011; @yildizActivatingSTAT6Mutations2015; @zhangGeneticHeterogeneityDiffuse2013]
12	12	15 studies for FL,[@barariaCathepsinAlterationsInduce2020; @cheungAcquiredTNFRSF14Mutations2010; @drevalGeneticSubdivisionsFollicular2023; @hubschmannMutationalMechanismsShaping2021; @krysiakRecurrentSomaticMutations2017; @laurentFollicularLymphomaComprises2024; @louissaintPediatrictypeNodalFollicular2016; @maSubtypespecificCooccurringGenetic2022; @morinFrequentMutationHistonemodifying2011; @morinSomaticMutationsAltering2010; @okosunRecurrentMTORC1activatingRRAGC2016; @pasqualucciInactivatingMutationsAcetyltransferase2011; @rossiAberrantSomaticHypermutation2006; @russler-germainMutationsAssociatedProgression2023; @yildizActivatingSTAT6Mutations2015] and 13 studies for BL.[@abateDistinctViralMutational2015; @burkhardtClinicalRelevanceMolecular2022; @grandeGenomewideDiscoverySomatic2019; @johnstonCmycHypermutationBurkitt1992; @loveGeneticLandscapeMutations2012; @maSubtypespecificCooccurringGenetic2022; @muppidiLossSignalingGa132014; @paneaWholeGenomeLandscape2019; @richterRecurrentMutationID32012; @schmitzBurkittLymphomaPathogenesis2012; @thomasGeneticSubgroupsInform2023; @wildaInactivationARFMDM2p53Pathway2004; @zhouSporadicEndemicBurkitt2019]
13	13
14	14	## Procedure for gene retirement (Tier 3)
...	...	@@ -89,13 +89,13 @@ The FLAGS rank of DLBCL genes in Tier 1, 2 and 3 is compared. The genes in the C
89	89
90	90	### CARD4 - pass
91	91
92		-![CARD4](primary/Love_CARD4.svg)
	92	+![](primary/Love_CARD4.svg)
93	93
94	94	Average rating: &starf; &starf; &starf; &starf; &star;
95	95
96	96	### ACAD9 - fail (insufficient support)
97	97
98		-![ACAD9](primary/Love_ACAD9.svg)
	98	+![](primary/Love_ACAD9.svg)
99	99
100	100	Average rating: &starf; &star; &star; &star; &star;
101	101