papers/burkhardtClinicalRelevanceMolecular2022.md
... ...
@@ -0,0 +1,64 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @burkhardtClinicalRelevanceMolecular2022b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|0|25|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 0
26
+New Tier 1, BL Tier 1, 0
27
+This study, New Tier 2, 25
28
+New Tier 2, BL Tier 2, 25
29
+All other BL studies, BL Tier 1, 29
30
+All other BL studies, BL Tier 2, 132
31
+```
32
+
33
+### Tier 2
34
+|New gene|BL tier|
35
+|:-|:-:|
36
+|[ADAMTS5](../ADAMTS5)|2 |
37
+|[ADNP](../ADNP)|2 |
38
+|[AGO4](../AGO4)|2 |
39
+|[BCL2](../BCL2)|2 |
40
+|[BTG1](../BTG1)|2 |
41
+|[CD79A](../CD79A)|2 |
42
+|[CHD4](../CHD4)|2 |
43
+|[CPXM2](../CPXM2)|2 |
44
+|[E2F2](../E2F2)|2 |
45
+|[EDNRB](../EDNRB)|2 |
46
+|[ERAP1](../ERAP1)|2 |
47
+|[HLA-DQB1](../HLA-DQB1)|2 |
48
+|[KLHL26](../KLHL26)|2 |
49
+|[NOA1](../NOA1)|2 |
50
+|[PIM1](../PIM1)|2 |
51
+|[PPP6R2](../PPP6R2)|2 |
52
+|[PREX1](../PREX1)|2 |
53
+|[REV3L](../REV3L)|2 |
54
+|[RPL10](../RPL10)|2 |
55
+|[SAL3](../SAL3)|2 |
56
+|[TTN](../TTN)|2 |
57
+|[VWA7](../VWA7)|2 |
58
+|[ZAN](../ZAN)|2 |
59
+|[ZBTB7A](../ZBTB7A)|2 |
60
+|[ZNF85](../ZNF85)|2 |
61
+
62
+
63
+# Details
64
+
papers/burkhardtClinicalRelevanceMolecular2022b.md
... ...
@@ -1,64 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @burkhardtClinicalRelevanceMolecular2022b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|0|25|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, BL Tier 1, 0
27
-This study, New Tier 2, 25
28
-New Tier 2, BL Tier 2, 25
29
-All other BL studies, BL Tier 1, 29
30
-All other BL studies, BL Tier 2, 132
31
-```
32
-
33
-### Tier 2
34
-|New gene|BL tier|
35
-|:-|:-:|
36
-|[ADAMTS5](../ADAMTS5)|2 |
37
-|[ADNP](../ADNP)|2 |
38
-|[AGO4](../AGO4)|2 |
39
-|[BCL2](../BCL2)|2 |
40
-|[BTG1](../BTG1)|2 |
41
-|[CD79A](../CD79A)|2 |
42
-|[CHD4](../CHD4)|2 |
43
-|[CPXM2](../CPXM2)|2 |
44
-|[E2F2](../E2F2)|2 |
45
-|[EDNRB](../EDNRB)|2 |
46
-|[ERAP1](../ERAP1)|2 |
47
-|[HLA-DQB1](../HLA-DQB1)|2 |
48
-|[KLHL26](../KLHL26)|2 |
49
-|[NOA1](../NOA1)|2 |
50
-|[PIM1](../PIM1)|2 |
51
-|[PPP6R2](../PPP6R2)|2 |
52
-|[PREX1](../PREX1)|2 |
53
-|[REV3L](../REV3L)|2 |
54
-|[RPL10](../RPL10)|2 |
55
-|[SAL3](../SAL3)|2 |
56
-|[TTN](../TTN)|2 |
57
-|[VWA7](../VWA7)|2 |
58
-|[ZAN](../ZAN)|2 |
59
-|[ZBTB7A](../ZBTB7A)|2 |
60
-|[ZNF85](../ZNF85)|2 |
61
-
62
-
63
-# Details
64
-
papers/chapuyMolecularSubtypesDiffuse2018.md
... ...
@@ -0,0 +1,71 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @chapuyMolecularSubtypesDiffuse2018b
7
+## Summary of novel genes
8
+
9
+|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail Rate|
10
+|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
11
+|DLBCL|19|2|17| 10\* | 7 | 41% |
12
+
13
+
14
+```mermaid
15
+---
16
+config:
17
+ sankey:
18
+ showValues: true
19
+ linkColor: target
20
+ width: 600
21
+ height: 300
22
+ nodeAlignment: right
23
+ prefix: '('
24
+ suffix: ' genes)'
25
+---
26
+sankey-beta
27
+New to this study, DLBCL Tier 1, 2
28
+New to this study, DLBCL Tier 2, 17
29
+DLBCL Tier 2, Pass QC, 10
30
+DLBCL Tier 2, Fail QC, 7
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|DLBCL tier|
37
+|:-|:-:|
38
+|[HIST1H1B](../HIST1H1B)|1 |
39
+|[LTB](../LTB)|1 |
40
+
41
+### Tier 2
42
+|Novel Gene|DLBCL tier|Average variant quality|QC outcome|
43
+|:-|:-:|:-:|:-:|
44
+|[GABRA2](../GABRA2)|2 |TBD|TBD|
45
+|[COQ7](../COQ7)|2 |★ ★ ★ ☆ ☆ |**Pass**|
46
+|[CRIP1](../CRIP1)|2 |★ ★ ★ ☆ ☆ |**Pass**|
47
+|[DOCK1](../DOCK1)|2 |★ ★ ★ ☆ ☆ |**Pass**|
48
+|[NAV1](../NAV1)|2 |TBD|TBD|
49
+|[IL6](../IL6)|2 |★ ★ ★ ☆ ☆ |**Pass**|
50
+|[LYN](../LYN)|2 |★ ★ ★ ★ ☆ |**Pass**|
51
+|[PRPS1](../PRPS1)|2 |★ ★ ★ ★ ☆ |**Pass**|
52
+|[TLR2](../TLR2)|2 |★ ★ ★ ★ ☆ |**Pass**|
53
+|[ZNF423](../ZNF423)|2 |★ ★ ★ ☆ ☆ |**Pass**|
54
+|[FUT5](../FUT5)|2 |★ ☆ ☆ ☆ ☆ |**Fail**|
55
+|[RAD9A](../RAD9A)|2 |*No variants reported*|**Fail**|
56
+|[CCL4](../CCL4)|2 |*No variants reported*|**Fail**|
57
+|[SMEK1](../SMEK1)|2 |*No variants in paired samples*|**Fail**|
58
+|[NANOG](../NANOG)|2 |*No variants reported*|**Fail**|
59
+|[NLRP8](../NLRP8)|2 |★ ★ ☆ ☆ ☆ |**Fail**|
60
+|[PDE4DIP](../PDE4DIP)|2 |★ ★ ☆ ☆ ☆ |**Fail**|
61
+
62
+
63
+## Data Availability
64
+
65
+|**Repository**|**Accession**|
66
+|-|-|
67
+|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v1.p1|
68
+|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v3.p1|
69
+
70
+# Details
71
+
papers/chapuyMolecularSubtypesDiffuse2018b.md
... ...
@@ -1,71 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @chapuyMolecularSubtypesDiffuse2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail Rate|
10
-|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
11
-|DLBCL|19|2|17| 10\* | 7 | 41% |
12
-
13
-
14
-```mermaid
15
----
16
-config:
17
- sankey:
18
- showValues: true
19
- linkColor: target
20
- width: 600
21
- height: 300
22
- nodeAlignment: right
23
- prefix: '('
24
- suffix: ' genes)'
25
----
26
-sankey-beta
27
-New to this study, DLBCL Tier 1, 2
28
-New to this study, DLBCL Tier 2, 17
29
-DLBCL Tier 2, Pass QC, 10
30
-DLBCL Tier 2, Fail QC, 7
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[HIST1H1B](../HIST1H1B)|1 |
39
-|[LTB](../LTB)|1 |
40
-
41
-### Tier 2
42
-|Novel Gene|DLBCL tier|Average variant quality|QC outcome|
43
-|:-|:-:|:-:|:-:|
44
-|[GABRA2](../GABRA2)|2 |TBD|TBD|
45
-|[COQ7](../COQ7)|2 |★ ★ ★ ☆ ☆ |**Pass**|
46
-|[CRIP1](../CRIP1)|2 |★ ★ ★ ☆ ☆ |**Pass**|
47
-|[DOCK1](../DOCK1)|2 |★ ★ ★ ☆ ☆ |**Pass**|
48
-|[NAV1](../NAV1)|2 |TBD|TBD|
49
-|[IL6](../IL6)|2 |★ ★ ★ ☆ ☆ |**Pass**|
50
-|[LYN](../LYN)|2 |★ ★ ★ ★ ☆ |**Pass**|
51
-|[PRPS1](../PRPS1)|2 |★ ★ ★ ★ ☆ |**Pass**|
52
-|[TLR2](../TLR2)|2 |★ ★ ★ ★ ☆ |**Pass**|
53
-|[ZNF423](../ZNF423)|2 |★ ★ ★ ☆ ☆ |**Pass**|
54
-|[FUT5](../FUT5)|2 |★ ☆ ☆ ☆ ☆ |**Fail**|
55
-|[RAD9A](../RAD9A)|2 |*No variants reported*|**Fail**|
56
-|[CCL4](../CCL4)|2 |*No variants reported*|**Fail**|
57
-|[SMEK1](../SMEK1)|2 |*No variants in paired samples*|**Fail**|
58
-|[NANOG](../NANOG)|2 |*No variants reported*|**Fail**|
59
-|[NLRP8](../NLRP8)|2 |★ ★ ☆ ☆ ☆ |**Fail**|
60
-|[PDE4DIP](../PDE4DIP)|2 |★ ★ ☆ ☆ ☆ |**Fail**|
61
-
62
-
63
-## Data Availability
64
-
65
-|**Repository**|**Accession**|
66
-|-|-|
67
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v1.p1|
68
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v3.p1|
69
-
70
-# Details
71
-
papers/dunsCharacterizationDLBCLPMBL2021.md
... ...
@@ -0,0 +1,60 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @dunsCharacterizationDLBCLPMBL2021b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|6|8|
12
+|DLBCL|8|3|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 6
27
+New Tier 1, PMBL Tier 1, 6
28
+This study, New Tier 2, 8
29
+New Tier 2, PMBL Tier 2, 8
30
+All other PMBL studies, PMBL Tier 1, 70
31
+All other PMBL studies, PMBL Tier 2, 74
32
+```
33
+
34
+## Novel genes reported in this study
35
+
36
+### Tier 1
37
+|New gene|PMBL tier|DLBCL tier|
38
+|:-|:-:|:-:|
39
+|[CD83](../CD83)|1 |1 |
40
+|[CREBBP](../CREBBP)|1 |1 |
41
+|[DUSP2](../DUSP2)|1 |1 |
42
+|[FOXO1](../FOXO1)|2 |1 |
43
+|[IL4R](../IL4R)|1 |1 |
44
+|[MYC](../MYC)|2 |1 |
45
+|[PIM1](../PIM1)|1 |1 |
46
+|[SGK1](../SGK1)|1 |1 |
47
+
48
+### Tier 2
49
+|New gene|PMBL tier|DLBCL tier|
50
+|:-|:-:|:-:|
51
+|[BIRC3](../BIRC3)|2 |2 |
52
+|[HRNR](../HRNR)|2 | |
53
+|[LPHN3](../LPHN3)|2 | |
54
+|[MCL1](../MCL1)|2 |2 |
55
+|[RFTN1](../RFTN1)|2 |2 |
56
+|[WDR87](../WDR87)|2 | |
57
+
58
+
59
+# Details
60
+
papers/dunsCharacterizationDLBCLPMBL2021b.md
... ...
@@ -1,60 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @dunsCharacterizationDLBCLPMBL2021b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|6|8|
12
-|DLBCL|8|3|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 6
27
-New Tier 1, PMBL Tier 1, 6
28
-This study, New Tier 2, 8
29
-New Tier 2, PMBL Tier 2, 8
30
-All other PMBL studies, PMBL Tier 1, 70
31
-All other PMBL studies, PMBL Tier 2, 74
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|PMBL tier|DLBCL tier|
38
-|:-|:-:|:-:|
39
-|[CD83](../CD83)|1 |1 |
40
-|[CREBBP](../CREBBP)|1 |1 |
41
-|[DUSP2](../DUSP2)|1 |1 |
42
-|[FOXO1](../FOXO1)|2 |1 |
43
-|[IL4R](../IL4R)|1 |1 |
44
-|[MYC](../MYC)|2 |1 |
45
-|[PIM1](../PIM1)|1 |1 |
46
-|[SGK1](../SGK1)|1 |1 |
47
-
48
-### Tier 2
49
-|New gene|PMBL tier|DLBCL tier|
50
-|:-|:-:|:-:|
51
-|[BIRC3](../BIRC3)|2 |2 |
52
-|[HRNR](../HRNR)|2 | |
53
-|[LPHN3](../LPHN3)|2 | |
54
-|[MCL1](../MCL1)|2 |2 |
55
-|[RFTN1](../RFTN1)|2 |2 |
56
-|[WDR87](../WDR87)|2 | |
57
-
58
-
59
-# Details
60
-
papers/fanComprehensiveCharacterizationDriver2020.md
... ...
@@ -0,0 +1,114 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @fanComprehensiveCharacterizationDriver2020b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|0|0|72|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 0
26
+New Tier 1, DLBCL Tier 1, 0
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 72
30
+New Tier 3, DLBCL Tier 3, 72
31
+All other DLBCL studies, DLBCL Tier 1, 127
32
+All other DLBCL studies, DLBCL Tier 2, 172
33
+All other DLBCL studies, DLBCL Tier 3, 309
34
+```
35
+
36
+### Tier 3
37
+|New gene|DLBCL tier|
38
+|:-|:-:|
39
+|[ABCB1](../ABCB1)|3 |
40
+|[AGA](../AGA)|3 |
41
+|[APMAP](../APMAP)|3 |
42
+|[ATP6V0A1](../ATP6V0A1)|3 |
43
+|[BRCA1](../BRCA1)|3 |
44
+|[CBX3](../CBX3)|3 |
45
+|[CDKN1A](../CDKN1A)|3 |
46
+|[CGN](../CGN)|3 |
47
+|[CHEK2](../CHEK2)|3 |
48
+|[CSNK1A1](../CSNK1A1)|3 |
49
+|[CSNK2A1](../CSNK2A1)|3 |
50
+|[CYYR1](../CYYR1)|3 |
51
+|[DGCR8](../DGCR8)|3 |
52
+|[DHX33](../DHX33)|3 |
53
+|[DOCK5](../DOCK5)|3 |
54
+|[ECT2L](../ECT2L)|3 |
55
+|[EGFR](../EGFR)|3 |
56
+|[FAIM](../FAIM)|3 |
57
+|[FAM161A](../FAM161A)|3 |
58
+|[FLNA](../FLNA)|3 |
59
+|[FLT1](../FLT1)|3 |
60
+|[FN1](../FN1)|3 |
61
+|[FZD1](../FZD1)|3 |
62
+|[GATA2](../GATA2)|3 |
63
+|[GATA3](../GATA3)|3 |
64
+|[HFE](../HFE)|3 |
65
+|[HLA-DRB1](../HLA-DRB1)|3 |
66
+|[IL6ST](../IL6ST)|3 |
67
+|[ITGB4](../ITGB4)|3 |
68
+|[ITPR1](../ITPR1)|3 |
69
+|[KITLG](../KITLG)|3 |
70
+|[KLRC4](../KLRC4)|3 |
71
+|[LEPR](../LEPR)|3 |
72
+|[MAP2K3](../MAP2K3)|3 |
73
+|[MCM8](../MCM8)|3 |
74
+|[MLH1](../MLH1)|3 |
75
+|[MMEL1](../MMEL1)|3 |
76
+|[MSN](../MSN)|3 |
77
+|[NOTCH3](../NOTCH3)|3 |
78
+|[NUP153](../NUP153)|3 |
79
+|[PABPC1](../PABPC1)|3 |
80
+|[PDGFRB](../PDGFRB)|3 |
81
+|[PFN1](../PFN1)|3 |
82
+|[PGR](../PGR)|3 |
83
+|[PLCB4](../PLCB4)|3 |
84
+|[PLCG2](../PLCG2)|3 |
85
+|[POLD3](../POLD3)|3 |
86
+|[POLQ](../POLQ)|3 |
87
+|[PPP2R2B](../PPP2R2B)|3 |
88
+|[PTCH1](../PTCH1)|3 |
89
+|[RAF1](../RAF1)|3 |
90
+|[RAPGEF3](../RAPGEF3)|3 |
91
+|[RECQL4](../RECQL4)|3 |
92
+|[RET](../RET)|3 |
93
+|[RHPN2](../RHPN2)|3 |
94
+|[RIF1](../RIF1)|3 |
95
+|[RIMS4](../RIMS4)|3 |
96
+|[RPTOR](../RPTOR)|3 |
97
+|[SLC16A8](../SLC16A8)|3 |
98
+|[SMO](../SMO)|3 |
99
+|[SOS2](../SOS2)|3 |
100
+|[TECRL](../TECRL)|3 |
101
+|[TLN1](../TLN1)|3 |
102
+|[TLR4](../TLR4)|3 |
103
+|[TNPO1](../TNPO1)|3 |
104
+|[TPR](../TPR)|3 |
105
+|[TYRO3](../TYRO3)|3 |
106
+|[UBXN11](../UBXN11)|3 |
107
+|[UBXN2B](../UBXN2B)|3 |
108
+|[VANGL1](../VANGL1)|3 |
109
+|[ZMYM4](../ZMYM4)|3 |
110
+|[ZNF814](../ZNF814)|3 |
111
+
112
+
113
+# Details
114
+
papers/fanComprehensiveCharacterizationDriver2020b.md
... ...
@@ -1,114 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @fanComprehensiveCharacterizationDriver2020b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
-|:-:|:-:|:-:|:-:|
11
-|DLBCL|0|0|72|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, DLBCL Tier 1, 0
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-This study, New Tier 3, 72
30
-New Tier 3, DLBCL Tier 3, 72
31
-All other DLBCL studies, DLBCL Tier 1, 127
32
-All other DLBCL studies, DLBCL Tier 2, 172
33
-All other DLBCL studies, DLBCL Tier 3, 309
34
-```
35
-
36
-### Tier 3
37
-|New gene|DLBCL tier|
38
-|:-|:-:|
39
-|[ABCB1](../ABCB1)|3 |
40
-|[AGA](../AGA)|3 |
41
-|[APMAP](../APMAP)|3 |
42
-|[ATP6V0A1](../ATP6V0A1)|3 |
43
-|[BRCA1](../BRCA1)|3 |
44
-|[CBX3](../CBX3)|3 |
45
-|[CDKN1A](../CDKN1A)|3 |
46
-|[CGN](../CGN)|3 |
47
-|[CHEK2](../CHEK2)|3 |
48
-|[CSNK1A1](../CSNK1A1)|3 |
49
-|[CSNK2A1](../CSNK2A1)|3 |
50
-|[CYYR1](../CYYR1)|3 |
51
-|[DGCR8](../DGCR8)|3 |
52
-|[DHX33](../DHX33)|3 |
53
-|[DOCK5](../DOCK5)|3 |
54
-|[ECT2L](../ECT2L)|3 |
55
-|[EGFR](../EGFR)|3 |
56
-|[FAIM](../FAIM)|3 |
57
-|[FAM161A](../FAM161A)|3 |
58
-|[FLNA](../FLNA)|3 |
59
-|[FLT1](../FLT1)|3 |
60
-|[FN1](../FN1)|3 |
61
-|[FZD1](../FZD1)|3 |
62
-|[GATA2](../GATA2)|3 |
63
-|[GATA3](../GATA3)|3 |
64
-|[HFE](../HFE)|3 |
65
-|[HLA-DRB1](../HLA-DRB1)|3 |
66
-|[IL6ST](../IL6ST)|3 |
67
-|[ITGB4](../ITGB4)|3 |
68
-|[ITPR1](../ITPR1)|3 |
69
-|[KITLG](../KITLG)|3 |
70
-|[KLRC4](../KLRC4)|3 |
71
-|[LEPR](../LEPR)|3 |
72
-|[MAP2K3](../MAP2K3)|3 |
73
-|[MCM8](../MCM8)|3 |
74
-|[MLH1](../MLH1)|3 |
75
-|[MMEL1](../MMEL1)|3 |
76
-|[MSN](../MSN)|3 |
77
-|[NOTCH3](../NOTCH3)|3 |
78
-|[NUP153](../NUP153)|3 |
79
-|[PABPC1](../PABPC1)|3 |
80
-|[PDGFRB](../PDGFRB)|3 |
81
-|[PFN1](../PFN1)|3 |
82
-|[PGR](../PGR)|3 |
83
-|[PLCB4](../PLCB4)|3 |
84
-|[PLCG2](../PLCG2)|3 |
85
-|[POLD3](../POLD3)|3 |
86
-|[POLQ](../POLQ)|3 |
87
-|[PPP2R2B](../PPP2R2B)|3 |
88
-|[PTCH1](../PTCH1)|3 |
89
-|[RAF1](../RAF1)|3 |
90
-|[RAPGEF3](../RAPGEF3)|3 |
91
-|[RECQL4](../RECQL4)|3 |
92
-|[RET](../RET)|3 |
93
-|[RHPN2](../RHPN2)|3 |
94
-|[RIF1](../RIF1)|3 |
95
-|[RIMS4](../RIMS4)|3 |
96
-|[RPTOR](../RPTOR)|3 |
97
-|[SLC16A8](../SLC16A8)|3 |
98
-|[SMO](../SMO)|3 |
99
-|[SOS2](../SOS2)|3 |
100
-|[TECRL](../TECRL)|3 |
101
-|[TLN1](../TLN1)|3 |
102
-|[TLR4](../TLR4)|3 |
103
-|[TNPO1](../TNPO1)|3 |
104
-|[TPR](../TPR)|3 |
105
-|[TYRO3](../TYRO3)|3 |
106
-|[UBXN11](../UBXN11)|3 |
107
-|[UBXN2B](../UBXN2B)|3 |
108
-|[VANGL1](../VANGL1)|3 |
109
-|[ZMYM4](../ZMYM4)|3 |
110
-|[ZNF814](../ZNF814)|3 |
111
-
112
-
113
-# Details
114
-
papers/krysiakRecurrentSomaticMutations2017.md
... ...
@@ -0,0 +1,67 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @krysiakRecurrentSomaticMutations2017b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|17|5|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 17
26
+New Tier 1, FL Tier 1, 17
27
+This study, New Tier 2, 5
28
+New Tier 2, FL Tier 2, 5
29
+All other FL studies, FL Tier 1, 49
30
+All other FL studies, FL Tier 2, 45
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|FL tier|
37
+|:-|:-:|
38
+|[ARID1A](../ARID1A)|1 |
39
+|[BCL7A](../BCL7A)|1 |
40
+|[BTK](../BTK)|1 |
41
+|[HIST1H1B](../HIST1H1B)|1 |
42
+|[HIST1H1D](../HIST1H1D)|1 |
43
+|[HIST1H1E](../HIST1H1E)|1 |
44
+|[HIST1H2AC](../HIST1H2AC)|1 |
45
+|[HIST1H2AG](../HIST1H2AG)|1 |
46
+|[HIST1H2AM](../HIST1H2AM)|1 |
47
+|[HIST1H2BC](../HIST1H2BC)|1 |
48
+|[HIST1H2BD](../HIST1H2BD)|1 |
49
+|[HIST1H2BG](../HIST1H2BG)|1 |
50
+|[HIST1H3G](../HIST1H3G)|1 |
51
+|[HVCN1](../HVCN1)|1 |
52
+|[POU2AF1](../POU2AF1)|1 |
53
+|[POU2F2](../POU2F2)|1 |
54
+|[SMARCA4](../SMARCA4)|1 |
55
+
56
+### Tier 2
57
+|New gene|FL tier|
58
+|:-|:-:|
59
+|[CXCR4](../CXCR4)|2 |
60
+|[EGR1](../EGR1)|2 |
61
+|[HIST1H2BM](../HIST1H2BM)|2 |
62
+|[HIST1H3I](../HIST1H3I)|2 |
63
+|[ZNF608](../ZNF608)|2 |
64
+
65
+
66
+# Details
67
+
papers/krysiakRecurrentSomaticMutations2017b.md
... ...
@@ -1,67 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @krysiakRecurrentSomaticMutations2017b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|17|5|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 17
26
-New Tier 1, FL Tier 1, 17
27
-This study, New Tier 2, 5
28
-New Tier 2, FL Tier 2, 5
29
-All other FL studies, FL Tier 1, 49
30
-All other FL studies, FL Tier 2, 45
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|FL tier|
37
-|:-|:-:|
38
-|[ARID1A](../ARID1A)|1 |
39
-|[BCL7A](../BCL7A)|1 |
40
-|[BTK](../BTK)|1 |
41
-|[HIST1H1B](../HIST1H1B)|1 |
42
-|[HIST1H1D](../HIST1H1D)|1 |
43
-|[HIST1H1E](../HIST1H1E)|1 |
44
-|[HIST1H2AC](../HIST1H2AC)|1 |
45
-|[HIST1H2AG](../HIST1H2AG)|1 |
46
-|[HIST1H2AM](../HIST1H2AM)|1 |
47
-|[HIST1H2BC](../HIST1H2BC)|1 |
48
-|[HIST1H2BD](../HIST1H2BD)|1 |
49
-|[HIST1H2BG](../HIST1H2BG)|1 |
50
-|[HIST1H3G](../HIST1H3G)|1 |
51
-|[HVCN1](../HVCN1)|1 |
52
-|[POU2AF1](../POU2AF1)|1 |
53
-|[POU2F2](../POU2F2)|1 |
54
-|[SMARCA4](../SMARCA4)|1 |
55
-
56
-### Tier 2
57
-|New gene|FL tier|
58
-|:-|:-:|
59
-|[CXCR4](../CXCR4)|2 |
60
-|[EGR1](../EGR1)|2 |
61
-|[HIST1H2BM](../HIST1H2BM)|2 |
62
-|[HIST1H3I](../HIST1H3I)|2 |
63
-|[ZNF608](../ZNF608)|2 |
64
-
65
-
66
-# Details
67
-
papers/kwanhianMicroRNA142Mutated202012.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @kwanhianMicroRNA142Mutated202012b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|DLBCL|0|1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 0
26
+New Tier 1, DLBCL Tier 1, 0
27
+This study, New Tier 2, 1
28
+New Tier 2, DLBCL Tier 2, 1
29
+All other DLBCL studies, DLBCL Tier 1, 128
30
+All other DLBCL studies, DLBCL Tier 2, 197
31
+```
32
+
33
+### Tier 2
34
+|New gene|DLBCL tier|
35
+|:-|:-:|
36
+|[MIR142](../MIR142)|2 |
37
+
38
+
39
+# Details
40
+
papers/kwanhianMicroRNA142Mutated202012b.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @kwanhianMicroRNA142Mutated202012b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|0|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, DLBCL Tier 1, 0
27
-This study, New Tier 2, 1
28
-New Tier 2, DLBCL Tier 2, 1
29
-All other DLBCL studies, DLBCL Tier 1, 128
30
-All other DLBCL studies, DLBCL Tier 2, 197
31
-```
32
-
33
-### Tier 2
34
-|New gene|DLBCL tier|
35
-|:-|:-:|
36
-|[MIR142](../MIR142)|2 |
37
-
38
-
39
-# Details
40
-
papers/mottokGenomicAlterationsCIITA2015.md
... ...
@@ -0,0 +1,42 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @mottokGenomicAlterationsCIITA2015b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+All other PMBL studies, PMBL Tier 1, 75
30
+All other PMBL studies, PMBL Tier 2, 82
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|PMBL tier|
37
+|:-|:-:|
38
+|[CIITA](../CIITA)|1 |
39
+
40
+
41
+# Details
42
+
papers/mottokGenomicAlterationsCIITA2015b.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @mottokGenomicAlterationsCIITA2015b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[CIITA](../CIITA)|1 |
39
-
40
-
41
-# Details
42
-
papers/muppidiLossSignalingGa132014.md
... ...
@@ -0,0 +1,48 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @muppidiLossSignalingGa132014b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|BL|1|2|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, BL Tier 1, 1
27
+This study, New Tier 2, 2
28
+New Tier 2, BL Tier 2, 2
29
+All other BL studies, BL Tier 1, 28
30
+All other BL studies, BL Tier 2, 155
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|BL tier|
37
+|:-|:-:|
38
+|[P2RY8](../P2RY8)|1 |
39
+
40
+### Tier 2
41
+|New gene|BL tier|
42
+|:-|:-:|
43
+|[ARHGEF1](../ARHGEF1)|2 |
44
+|[S1PR2](../S1PR2)|2 |
45
+
46
+
47
+# Details
48
+
papers/muppidiLossSignalingGa132014b.md
... ...
@@ -1,48 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @muppidiLossSignalingGa132014b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, BL Tier 1, 1
27
-This study, New Tier 2, 2
28
-New Tier 2, BL Tier 2, 2
29
-All other BL studies, BL Tier 1, 28
30
-All other BL studies, BL Tier 2, 155
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|BL tier|
37
-|:-|:-:|
38
-|[P2RY8](../P2RY8)|1 |
39
-
40
-### Tier 2
41
-|New gene|BL tier|
42
-|:-|:-:|
43
-|[ARHGEF1](../ARHGEF1)|2 |
44
-|[S1PR2](../S1PR2)|2 |
45
-
46
-
47
-# Details
48
-
papers/nadeuGenomicEpigenomicInsights2020.md
... ...
@@ -0,0 +1,50 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @nadeuGenomicEpigenomicInsights2020b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|MCL|3|2|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 3
26
+New Tier 1, MCL Tier 1, 3
27
+This study, New Tier 2, 2
28
+New Tier 2, MCL Tier 2, 2
29
+All other MCL studies, MCL Tier 1, 20
30
+All other MCL studies, MCL Tier 2, 44
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|MCL tier|
37
+|:-|:-:|
38
+|[SMARCA4](../SMARCA4)|1 |
39
+|[SYNE1](../SYNE1)|1 |
40
+|[TERT](../TERT)|1 |
41
+
42
+### Tier 2
43
+|New gene|MCL tier|
44
+|:-|:-:|
45
+|[BCOR](../BCOR)|2 |
46
+|[SMARCB1](../SMARCB1)|2 |
47
+
48
+
49
+# Details
50
+
papers/nadeuGenomicEpigenomicInsights2020b.md
... ...
@@ -1,50 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @nadeuGenomicEpigenomicInsights2020b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|3|2|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 3
26
-New Tier 1, MCL Tier 1, 3
27
-This study, New Tier 2, 2
28
-New Tier 2, MCL Tier 2, 2
29
-All other MCL studies, MCL Tier 1, 20
30
-All other MCL studies, MCL Tier 2, 44
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|MCL tier|
37
-|:-|:-:|
38
-|[SMARCA4](../SMARCA4)|1 |
39
-|[SYNE1](../SYNE1)|1 |
40
-|[TERT](../TERT)|1 |
41
-
42
-### Tier 2
43
-|New gene|MCL tier|
44
-|:-|:-:|
45
-|[BCOR](../BCOR)|2 |
46
-|[SMARCB1](../SMARCB1)|2 |
47
-
48
-
49
-# Details
50
-
papers/oricchioGeneticEpigeneticInactivation2017.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @oricchioGeneticEpigeneticInactivation2017b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|0|1|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 0
26
+New Tier 1, FL Tier 1, 0
27
+This study, New Tier 2, 1
28
+New Tier 2, FL Tier 2, 1
29
+All other FL studies, FL Tier 1, 66
30
+All other FL studies, FL Tier 2, 49
31
+```
32
+
33
+### Tier 2
34
+|New gene|FL tier|
35
+|:-|:-:|
36
+|[SESN1](../SESN1)|2 |
37
+
38
+
39
+# Details
40
+
papers/oricchioGeneticEpigeneticInactivation2017b.md
... ...
@@ -1,40 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @oricchioGeneticEpigeneticInactivation2017b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|0|1|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, FL Tier 1, 0
27
-This study, New Tier 2, 1
28
-New Tier 2, FL Tier 2, 1
29
-All other FL studies, FL Tier 1, 66
30
-All other FL studies, FL Tier 2, 49
31
-```
32
-
33
-### Tier 2
34
-|New gene|FL tier|
35
-|:-|:-:|
36
-|[SESN1](../SESN1)|2 |
37
-
38
-
39
-# Details
40
-
papers/russler-germainMutationsAssociatedProgression2023.md
... ...
@@ -0,0 +1,65 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @russler-germainMutationsAssociatedProgression2023b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|FL|1|19|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, FL Tier 1, 1
27
+This study, New Tier 2, 19
28
+New Tier 2, FL Tier 2, 19
29
+All other FL studies, FL Tier 1, 65
30
+All other FL studies, FL Tier 2, 31
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|FL tier|
37
+|:-|:-:|
38
+|[CD83](../CD83)|1 |
39
+
40
+### Tier 2
41
+|New gene|FL tier|
42
+|:-|:-:|
43
+|[ABL2](../ABL2)|2 |
44
+|[BCL10](../BCL10)|2 |
45
+|[CD70](../CD70)|2 |
46
+|[CILP](../CILP)|2 |
47
+|[CYP2A6](../CYP2A6)|2 |
48
+|[GBP7](../GBP7)|2 |
49
+|[GRM6](../GRM6)|2 |
50
+|[IGLL5](../IGLL5)|2 |
51
+|[KIR3DL1](../KIR3DL1)|2 |
52
+|[MAGEC1](../MAGEC1)|2 |
53
+|[MAP7D1](../MAP7D1)|2 |
54
+|[MKI67](../MKI67)|2 |
55
+|[NFKBIA](../NFKBIA)|2 |
56
+|[OR8H2](../OR8H2)|2 |
57
+|[PZP](../PZP)|2 |
58
+|[SHROOM3](../SHROOM3)|2 |
59
+|[SRRM2](../SRRM2)|2 |
60
+|[STAB2](../STAB2)|2 |
61
+|[XIRP2](../XIRP2)|2 |
62
+
63
+
64
+# Details
65
+
papers/russler-germainMutationsAssociatedProgression2023b.md
... ...
@@ -1,65 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @russler-germainMutationsAssociatedProgression2023b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|19|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, FL Tier 1, 1
27
-This study, New Tier 2, 19
28
-New Tier 2, FL Tier 2, 19
29
-All other FL studies, FL Tier 1, 65
30
-All other FL studies, FL Tier 2, 31
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|FL tier|
37
-|:-|:-:|
38
-|[CD83](../CD83)|1 |
39
-
40
-### Tier 2
41
-|New gene|FL tier|
42
-|:-|:-:|
43
-|[ABL2](../ABL2)|2 |
44
-|[BCL10](../BCL10)|2 |
45
-|[CD70](../CD70)|2 |
46
-|[CILP](../CILP)|2 |
47
-|[CYP2A6](../CYP2A6)|2 |
48
-|[GBP7](../GBP7)|2 |
49
-|[GRM6](../GRM6)|2 |
50
-|[IGLL5](../IGLL5)|2 |
51
-|[KIR3DL1](../KIR3DL1)|2 |
52
-|[MAGEC1](../MAGEC1)|2 |
53
-|[MAP7D1](../MAP7D1)|2 |
54
-|[MKI67](../MKI67)|2 |
55
-|[NFKBIA](../NFKBIA)|2 |
56
-|[OR8H2](../OR8H2)|2 |
57
-|[PZP](../PZP)|2 |
58
-|[SHROOM3](../SHROOM3)|2 |
59
-|[SRRM2](../SRRM2)|2 |
60
-|[STAB2](../STAB2)|2 |
61
-|[XIRP2](../XIRP2)|2 |
62
-
63
-
64
-# Details
65
-
papers/tiacciPervasiveMutationsJAKSTAT2018.md
... ...
@@ -0,0 +1,55 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @tiacciPervasiveMutationsJAKSTAT2018b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1|9|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 9
28
+New Tier 2, PMBL Tier 2, 9
29
+All other PMBL studies, PMBL Tier 1, 75
30
+All other PMBL studies, PMBL Tier 2, 73
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|PMBL tier|
37
+|:-|:-:|
38
+|[TP53](../TP53)|1 |
39
+
40
+### Tier 2
41
+|New gene|PMBL tier|
42
+|:-|:-:|
43
+|[AKAP6](../AKAP6)|2 |
44
+|[DGKB](../DGKB)|2 |
45
+|[ITPR3](../ITPR3)|2 |
46
+|[NUP214](../NUP214)|2 |
47
+|[PRUNE2](../PRUNE2)|2 |
48
+|[SETD5](../SETD5)|2 |
49
+|[STAT5B](../STAT5B)|2 |
50
+|[TNIP1](../TNIP1)|2 |
51
+|[ZCCHC11](../ZCCHC11)|2 |
52
+
53
+
54
+# Details
55
+
papers/tiacciPervasiveMutationsJAKSTAT2018b.md
... ...
@@ -1,55 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @tiacciPervasiveMutationsJAKSTAT2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|9|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 9
28
-New Tier 2, PMBL Tier 2, 9
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 73
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[TP53](../TP53)|1 |
39
-
40
-### Tier 2
41
-|New gene|PMBL tier|
42
-|:-|:-:|
43
-|[AKAP6](../AKAP6)|2 |
44
-|[DGKB](../DGKB)|2 |
45
-|[ITPR3](../ITPR3)|2 |
46
-|[NUP214](../NUP214)|2 |
47
-|[PRUNE2](../PRUNE2)|2 |
48
-|[SETD5](../SETD5)|2 |
49
-|[STAT5B](../STAT5B)|2 |
50
-|[TNIP1](../TNIP1)|2 |
51
-|[ZCCHC11](../ZCCHC11)|2 |
52
-
53
-
54
-# Details
55
-
papers/viganoSomaticIL4RMutations2018.md
... ...
@@ -0,0 +1,42 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @viganoSomaticIL4RMutations2018b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|1|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, PMBL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, PMBL Tier 2, 0
29
+All other PMBL studies, PMBL Tier 1, 75
30
+All other PMBL studies, PMBL Tier 2, 82
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|PMBL tier|
37
+|:-|:-:|
38
+|[IL4R](../IL4R)|1 |
39
+
40
+
41
+# Details
42
+
papers/viganoSomaticIL4RMutations2018b.md
... ...
@@ -1,42 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @viganoSomaticIL4RMutations2018b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, PMBL Tier 1, 1
27
-This study, New Tier 2, 0
28
-New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[IL4R](../IL4R)|1 |
39
-
40
-
41
-# Details
42
-
papers/wienandGenomicAnalysesFlowsorted2019.md
... ...
@@ -0,0 +1,52 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @wienandGenomicAnalysesFlowsorted2019b
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|
10
+|:-:|:-:|:-:|
11
+|PMBL|4|3|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 4
26
+New Tier 1, PMBL Tier 1, 4
27
+This study, New Tier 2, 3
28
+New Tier 2, PMBL Tier 2, 3
29
+All other PMBL studies, PMBL Tier 1, 72
30
+All other PMBL studies, PMBL Tier 2, 79
31
+```
32
+
33
+## Novel genes reported in this study
34
+
35
+### Tier 1
36
+|New gene|PMBL tier|
37
+|:-|:-:|
38
+|[ACTB](../ACTB)|1 |
39
+|[ARID1A](../ARID1A)|1 |
40
+|[HLA-B](../HLA-B)|1 |
41
+|[NFKBIA](../NFKBIA)|1 |
42
+
43
+### Tier 2
44
+|New gene|PMBL tier|
45
+|:-|:-:|
46
+|[DNAH12](../DNAH12)|2 |
47
+|[IKBKB](../IKBKB)|2 |
48
+|[RBM38](../RBM38)|2 |
49
+
50
+
51
+# Details
52
+
papers/wienandGenomicAnalysesFlowsorted2019b.md
... ...
@@ -1,52 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @wienandGenomicAnalysesFlowsorted2019b
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|4|3|
12
-```mermaid
13
----
14
-config:
15
- sankey:
16
- showValues: true
17
- linkColor: target
18
- width: 600
19
- height: 300
20
- nodeAlignment: right
21
- prefix: '('
22
- suffix: ' genes)'
23
----
24
-sankey-beta
25
-This study, New Tier 1, 4
26
-New Tier 1, PMBL Tier 1, 4
27
-This study, New Tier 2, 3
28
-New Tier 2, PMBL Tier 2, 3
29
-All other PMBL studies, PMBL Tier 1, 72
30
-All other PMBL studies, PMBL Tier 2, 79
31
-```
32
-
33
-## Novel genes reported in this study
34
-
35
-### Tier 1
36
-|New gene|PMBL tier|
37
-|:-|:-:|
38
-|[ACTB](../ACTB)|1 |
39
-|[ARID1A](../ARID1A)|1 |
40
-|[HLA-B](../HLA-B)|1 |
41
-|[NFKBIA](../NFKBIA)|1 |
42
-
43
-### Tier 2
44
-|New gene|PMBL tier|
45
-|:-|:-:|
46
-|[DNAH12](../DNAH12)|2 |
47
-|[IKBKB](../IKBKB)|2 |
48
-|[RBM38](../RBM38)|2 |
49
-
50
-
51
-# Details
52
-