Changes in 03ff6f0: Fix

				tables/DLBCL_genes.md
			
          @@ -1,26 +0,0 @@

          ----

          -title: 'DLBCL genes'

          -bibliography: 'morinlab.bib'

          -csl: 'NLM.csl'

          -link-citations: true

          -nocite: |

          -  @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

          ----

          -

          -## Origins of DLBCL genes

          -

          -![](DLBCL_sankey-1.svg)

          -

          -## Tier 1 DLBCL genes

          -

          -[[include:DLBCL_Tier1.md]]

          -

          -## Tier 2 DLBCL genes

          -

          -[[include:DLBCL_Tier2.md]]

          -

          -## Tier 3 DLBCL genes

          -

          -[[include:DLBCL_Tier3.md]]

          -

          -## References

          \ No newline at end of file

				tables/DLBCL_sankey1.md
			
          @@ -1,85 +0,0 @@

          -

          -

          -```mermaid

          -

          -

          ----

          -config:

          -  sankey:

          -    showValues: false

          -    linkColor: target

          -    width: 800

          -    height: 1000

          -    nodeAlignment: right

          ----

          -sankey-beta

          -

          -RNA-seq/WGS, 2011, 25

          -2011, morin 2011, 25

          -morin 2011, Tier 1 DLBCL genes, 25

          -

          -exome, 2011, 9

          -2011, pasqualucci 2011a, 7

          -pasqualucci 2011a, Tier 1 DLBCL genes, 5

          -pasqualucci 2011a, Tier 2 DLBCL genes, 2

          -2011, pasqualucci 2011b, 2

          -pasqualucci 2011b, Tier 1 DLBCL genes, 2

          -

          -exome, 2012 exome studies, 4

          -2012 exome studies, lohr 2012, 4

          -lohr 2012, Tier 2 DLBCL genes, 1

          -lohr 2012, Tier 1 DLBCL genes, 3

          -

          -

          -WGS, 2013 WGS studies, 40

          -2013 WGS studies, morin 2013, 40

          -morin 2013, Tier 2 DLBCL genes, 29

          -morin 2013, Tier 1 DLBCL genes, 11

          -

          -exome, 2013 exome studies, 19

          -2013 exome studies, zhang 2013, 19

          -zhang 2013,  Tier 1 DLBCL genes, 11

          -zhang 2013,  Tier 2 DLBCL genes, 8

          -

          -

          -exome, 2016 exome studies, 2

          -2016 exome studies, mareschal 2016, 2

          -mareschal 2016, Tier 1 DLBCL genes, 2

          -

          -exome, 2016 exome studies, 2

          -2016 exome studies, morin 2016, 2

          -morin 2016, Tier 1 DLBCL genes, 2

          -

          -2017 exome studies, albuquerque 2017, 3

          -albuquerque 2017, Tier 1 DLBCL genes, 3

          -

          -exome, 2017 exome studies, 63

          -2017 exome studies, reddy 2017, 60

          -reddy 2017, Tier 2 DLBCL genes, 50

          -reddy 2017, Tier 1 DLBCL genes, 10

          -

          -exome, 2018 exome studies, 35

          -2018 exome studies, schmitz 2018, 16

          -schmitz 2018, Tier 2 DLBCL genes, 7

          -schmitz 2018, Tier 1 DLBCL genes, 9

          -

          -2018 exome studies, chapuy 2018, 19

          -chapuy 2018, Tier 2 DLBCL genes, 16

          -chapuy 2018, Tier 1 DLBCL genes, 3

          -

          -WGS, 2018 WGS studies, 20

          -2018 WGS studies, arthur 2018, 20

          -arthur 2018, Tier 2 DLBCL genes, 12

          -arthur 2018, Tier 1 DLBCL genes, 8

          -

          -exome, 2020-exome, 2

          -2020-exome, pararajalingam 2020, 2

          -pararajalingam 2020, Tier 1 DLBCL genes, 2

          -

          -WGS, 2021-WGS, 23

          -2021-WGS, hubschmann 2021, 23

          -hubschmann 2021, Tier 1 DLBCL genes, 4

          -hubschmann 2021, Tier 2 DLBCL genes, 19

          -

          -

          -```

				tables/DLBCL_tier1_sankey.md
			
          @@ -1,85 +0,0 @@

          -

          -

          -```mermaid

          -

          -

          ----

          -config:

          -  sankey:

          -    showValues: false

          -    linkColor: target

          -    width: 800

          -    height: 1000

          -    nodeAlignment: right

          ----

          -sankey-beta

          -

          -RNA-seq/WGS, 2011, 25

          -2011, morin 2011, 25

          -morin 2011, Tier 1 DLBCL genes, 25

          -

          -exome, 2011, 9

          -2011, pasqualucci 2011a, 7

          -pasqualucci 2011a, Tier 1 DLBCL genes, 5

          -

          -2011, pasqualucci 2011b, 2

          -pasqualucci 2011b, Tier 1 DLBCL genes, 2

          -

          -exome, 2012 exome studies, 4

          -2012 exome studies, lohr 2012, 4

          -

          -lohr 2012, Tier 1 DLBCL genes, 3

          -

          -

          -WGS, 2013 WGS studies, 40

          -2013 WGS studies, morin 2013, 40

          -

          -morin 2013, Tier 1 DLBCL genes, 11

          -

          -exome, 2013 exome studies, 19

          -2013 exome studies, zhang 2013, 19

          -zhang 2013,  Tier 1 DLBCL genes, 11

          -

          -

          -

          -exome, 2016 exome studies, 2

          -2016 exome studies, mareschal 2016, 2

          -mareschal 2016, Tier 1 DLBCL genes, 2

          -

          -exome, 2016 exome studies, 2

          -2016 exome studies, morin 2016, 2

          -morin 2016, Tier 1 DLBCL genes, 2

          -

          -2017 exome studies, albuquerque 2017, 3

          -albuquerque 2017, Tier 1 DLBCL genes, 3

          -

          -exome, 2017 exome studies, 63

          -2017 exome studies, reddy 2017, 60

          -

          -reddy 2017, Tier 1 DLBCL genes, 10

          -

          -exome, 2018 exome studies, 35

          -2018 exome studies, schmitz 2018, 16

          -

          -schmitz 2018, Tier 1 DLBCL genes, 9

          -

          -2018 exome studies, chapuy 2018, 19

          -

          -chapuy 2018, Tier 1 DLBCL genes, 3

          -

          -WGS, 2018 WGS studies, 20

          -2018 WGS studies, arthur 2018, 20

          -

          -arthur 2018, Tier 1 DLBCL genes, 8

          -

          -exome, 2020-exome, 2

          -2020-exome, pararajalingam 2020, 2

          -pararajalingam 2020, Tier 1 DLBCL genes, 2

          -

          -WGS, 2021-WGS, 23

          -2021-WGS, hubschmann 2021, 23

          -hubschmann 2021, Tier 1 DLBCL genes, 4

          -

          -

          -

          -```

				tables/FL_genes.md
			
          @@ -1,27 +0,0 @@

          ----

          -title: 'FL genes'

          -bibliography: 'morinlab.bib'

          -csl: 'NLM.csl'

          -link-citations: true

          -nocite: |

          -  @barariaCathepsinAlterationsInduce2020, @cheungAcquiredTNFRSF14Mutations2010, @drevalGeneticSubdivisionsFollicular2023, @greenMutationsEarlyFollicular2015, @hubschmannMutationalMechanismsShaping2021, @krysiakRecurrentSomaticMutations2017, @laurentFollicularLymphomaComprises2024, @louissaintPediatrictypeNodalFollicular2016, @maSubtypespecificCooccurringGenetic2022, @morinFrequentMutationHistonemodifying2011, @morinSomaticMutationsAltering2010, @okosunRecurrentMTORC1activatingRRAGC2016, @pasqualucciInactivatingMutationsAcetyltransferase2011, @rossiAberrantSomaticHypermutation2006, @russler-germainMutationsAssociatedProgression2023, @yildizActivatingSTAT6Mutations2015

          ----

          -

          -## Origins of FL genes

          -

          -![](FL_sankey-1.svg)

          -

          -

          -## Tier 1 FL genes

          -

          -[[include:FL_Tier1.md]]

          -

          -## Tier 2 FL genes

          -

          -[[include:FL_Tier2.md]]

          -

          -## Tier 3 FL genes

          -

          -[[include:FL_Tier3.md]]

          -

          -# References

				tables/FL_sankey.md
			
          @@ -1,34 +0,0 @@

          -```mermaid

          ----

          -config:

          -  sankey:

          -    showValues: false

          -    linkColor: target

          -    width: 800

          -    height: 1000

          -    nodeAlignment: right

          ----

          -sankey-beta

          -Krysiak 2017, FL Tier 1, 17

          -Krysiak 2017, FL Tier 2, 5

          -Morin 2011, FL Tier 1, 14

          -Morin 2011, FL Tier 2, 1

          -Hubschmann 2021, FL Tier 1, 2

          -Hubschmann 2021, FL Tier 2, 15

          -Pasqualucci 2011, FL Tier 1, 2

          -Russler-germain 2023, FL Tier 1, 1

          -Russler-germain 2023, FL Tier 2, 19

          -Okosun 2016, FL Tier 1, 2

          -FL, WGS, 2

          -WGS, Okosun 2016, 2

          -FL, exome, 20

          -exome, Russler-germain 2023, 20

          -FL, exome, 2

          -exome, Pasqualucci 2011, 2

          -FL, WGS, 17

          -WGS, Hubschmann 2021, 17

          -FL, RNA-seq/WGS, 15

          -RNA-seq/WGS, Morin 2011, 15

          -FL, exome, 22

          -exome, Krysiak 2017, 22

          -```

				tables/FL_test_sankey.md
			
          @@ -1,16 +0,0 @@

          -```mermaid

          ----

          -config:

          -  sankey:

          -    showValues: true

          -    linkColor: target

          -    width: 600

          -    nodeAlignment: right

          ----

          -sankey-beta

          -FL, GC-like, 56

          -FL, MEM-like, 50

          -GC-like, dFL, 37 

          -GC-like, cFL, 19 

          -MEM-like, dFL, 17 

          -MEM-like, cFL, 33

...	...	@@ -1,26 +0,0 @@
1		----
2		-title: 'DLBCL genes'
3		-bibliography: 'morinlab.bib'
4		-csl: 'NLM.csl'
5		-link-citations: true
6		-nocite: \|
7		- @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
8		----
9		-
10		-## Origins of DLBCL genes
11		-
12		-![](DLBCL_sankey-1.svg)
13		-
14		-## Tier 1 DLBCL genes
15		-
16		-[[include:DLBCL_Tier1.md]]
17		-
18		-## Tier 2 DLBCL genes
19		-
20		-[[include:DLBCL_Tier2.md]]
21		-
22		-## Tier 3 DLBCL genes
23		-
24		-[[include:DLBCL_Tier3.md]]
25		-
26		-## References
...	...	\ No newline at end of file

...	...	@@ -1,85 +0,0 @@
1		-
2		-
3		-```mermaid
4		-
5		-
6		----
7		-config:
8		- sankey:
9		- showValues: false
10		- linkColor: target
11		- width: 800
12		- height: 1000
13		- nodeAlignment: right
14		----
15		-sankey-beta
16		-
17		-RNA-seq/WGS, 2011, 25
18		-2011, morin 2011, 25
19		-morin 2011, Tier 1 DLBCL genes, 25
20		-
21		-exome, 2011, 9
22		-2011, pasqualucci 2011a, 7
23		-pasqualucci 2011a, Tier 1 DLBCL genes, 5
24		-pasqualucci 2011a, Tier 2 DLBCL genes, 2
25		-2011, pasqualucci 2011b, 2
26		-pasqualucci 2011b, Tier 1 DLBCL genes, 2
27		-
28		-exome, 2012 exome studies, 4
29		-2012 exome studies, lohr 2012, 4
30		-lohr 2012, Tier 2 DLBCL genes, 1
31		-lohr 2012, Tier 1 DLBCL genes, 3
32		-
33		-
34		-WGS, 2013 WGS studies, 40
35		-2013 WGS studies, morin 2013, 40
36		-morin 2013, Tier 2 DLBCL genes, 29
37		-morin 2013, Tier 1 DLBCL genes, 11
38		-
39		-exome, 2013 exome studies, 19
40		-2013 exome studies, zhang 2013, 19
41		-zhang 2013, Tier 1 DLBCL genes, 11
42		-zhang 2013, Tier 2 DLBCL genes, 8
43		-
44		-
45		-exome, 2016 exome studies, 2
46		-2016 exome studies, mareschal 2016, 2
47		-mareschal 2016, Tier 1 DLBCL genes, 2
48		-
49		-exome, 2016 exome studies, 2
50		-2016 exome studies, morin 2016, 2
51		-morin 2016, Tier 1 DLBCL genes, 2
52		-
53		-2017 exome studies, albuquerque 2017, 3
54		-albuquerque 2017, Tier 1 DLBCL genes, 3
55		-
56		-exome, 2017 exome studies, 63
57		-2017 exome studies, reddy 2017, 60
58		-reddy 2017, Tier 2 DLBCL genes, 50
59		-reddy 2017, Tier 1 DLBCL genes, 10
60		-
61		-exome, 2018 exome studies, 35
62		-2018 exome studies, schmitz 2018, 16
63		-schmitz 2018, Tier 2 DLBCL genes, 7
64		-schmitz 2018, Tier 1 DLBCL genes, 9
65		-
66		-2018 exome studies, chapuy 2018, 19
67		-chapuy 2018, Tier 2 DLBCL genes, 16
68		-chapuy 2018, Tier 1 DLBCL genes, 3
69		-
70		-WGS, 2018 WGS studies, 20
71		-2018 WGS studies, arthur 2018, 20
72		-arthur 2018, Tier 2 DLBCL genes, 12
73		-arthur 2018, Tier 1 DLBCL genes, 8
74		-
75		-exome, 2020-exome, 2
76		-2020-exome, pararajalingam 2020, 2
77		-pararajalingam 2020, Tier 1 DLBCL genes, 2
78		-
79		-WGS, 2021-WGS, 23
80		-2021-WGS, hubschmann 2021, 23
81		-hubschmann 2021, Tier 1 DLBCL genes, 4
82		-hubschmann 2021, Tier 2 DLBCL genes, 19
83		-
84		-
85		-```

...	...	@@ -1,27 +0,0 @@
1		----
2		-title: 'FL genes'
3		-bibliography: 'morinlab.bib'
4		-csl: 'NLM.csl'
5		-link-citations: true
6		-nocite: \|
7		- @barariaCathepsinAlterationsInduce2020, @cheungAcquiredTNFRSF14Mutations2010, @drevalGeneticSubdivisionsFollicular2023, @greenMutationsEarlyFollicular2015, @hubschmannMutationalMechanismsShaping2021, @krysiakRecurrentSomaticMutations2017, @laurentFollicularLymphomaComprises2024, @louissaintPediatrictypeNodalFollicular2016, @maSubtypespecificCooccurringGenetic2022, @morinFrequentMutationHistonemodifying2011, @morinSomaticMutationsAltering2010, @okosunRecurrentMTORC1activatingRRAGC2016, @pasqualucciInactivatingMutationsAcetyltransferase2011, @rossiAberrantSomaticHypermutation2006, @russler-germainMutationsAssociatedProgression2023, @yildizActivatingSTAT6Mutations2015
8		----
9		-
10		-## Origins of FL genes
11		-
12		-![](FL_sankey-1.svg)
13		-
14		-
15		-## Tier 1 FL genes
16		-
17		-[[include:FL_Tier1.md]]
18		-
19		-## Tier 2 FL genes
20		-
21		-[[include:FL_Tier2.md]]
22		-
23		-## Tier 3 FL genes
24		-
25		-[[include:FL_Tier3.md]]
26		-
27		-# References

...	...	@@ -1,34 +0,0 @@
1		-```mermaid
2		----
3		-config:
4		- sankey:
5		- showValues: false
6		- linkColor: target
7		- width: 800
8		- height: 1000
9		- nodeAlignment: right
10		----
11		-sankey-beta
12		-Krysiak 2017, FL Tier 1, 17
13		-Krysiak 2017, FL Tier 2, 5
14		-Morin 2011, FL Tier 1, 14
15		-Morin 2011, FL Tier 2, 1
16		-Hubschmann 2021, FL Tier 1, 2
17		-Hubschmann 2021, FL Tier 2, 15
18		-Pasqualucci 2011, FL Tier 1, 2
19		-Russler-germain 2023, FL Tier 1, 1
20		-Russler-germain 2023, FL Tier 2, 19
21		-Okosun 2016, FL Tier 1, 2
22		-FL, WGS, 2
23		-WGS, Okosun 2016, 2
24		-FL, exome, 20
25		-exome, Russler-germain 2023, 20
26		-FL, exome, 2
27		-exome, Pasqualucci 2011, 2
28		-FL, WGS, 17
29		-WGS, Hubschmann 2021, 17
30		-FL, RNA-seq/WGS, 15
31		-RNA-seq/WGS, Morin 2011, 15
32		-FL, exome, 22
33		-exome, Krysiak 2017, 22
34		-```

...	...	@@ -1,16 +0,0 @@
1		-```mermaid
2		----
3		-config:
4		- sankey:
5		- showValues: true
6		- linkColor: target
7		- width: 600
8		- nodeAlignment: right
9		----
10		-sankey-beta
11		-FL, GC-like, 56
12		-FL, MEM-like, 50
13		-GC-like, dFL, 37
14		-GC-like, cFL, 19
15		-MEM-like, dFL, 17
16		-MEM-like, cFL, 33