MutSig results for PRAD

Number of individuals: 83

Summary of findings

Significantly mutated genes (q≤0.1) 36
Mutations seen in COSMIC 0
Significantly mutated genes on COSMIC territory 0
Genes with clustered mutations (≤3 aa apart) 1
Significantly mutated genesets 8
. . . . . . . . . (excluding sig.mutated genes) 3

Mutation preprocessing

Read 83 MAFs of type "Broad"
Total number of mutations in input MAFs:	12281
After removing 6684 noncoding mutations:	5597
After collapsing adjacent/redundant mutations:	5568

Please see MutSigPreprocess "stdout.txt" for full details.

Mutation filtering

Number of mutations before filtering:		5568
After removing 268 mutations outside gene set:	5300
After removing 1367 mutations outside category set:	3933

Please see MutSigRun "stdout.txt" for full details.

Final mutation list

Final set of mutations used in analysis

Mutation breakdown by type

type count
Frame_Shift_Del 152
Frame_Shift_Ins 79
In_Frame_Del 51
In_Frame_Ins 12
Missense_Mutation 2364
Nonsense_Mutation 137
Nonstop_Mutation 1
Silent 1051
Splice_Site 77
Translation_Start_Site 9
Total 3933

type	count
Frame_Shift_Del	152
Frame_Shift_Ins	79
In_Frame_Del	51
In_Frame_Ins	12
Missense_Mutation	2364
Nonsense_Mutation	137
Nonstop_Mutation	1
Silent	1051
Splice_Site	77
Translation_Start_Site	9
Total	3933

Nonsilent mutations: categories and mutation rates

category n N rate rate_per_mb relative_rate
A->T 610 1,231,130,036 4.95e-07 0.50 0.43
C->(A/T) 898 1,294,928,235 6.93e-07 0.69 0.61
A->(C/G) 622 1,231,130,036 5.05e-07 0.51 0.44
C->G 239 1,294,928,235 1.85e-07 0.18 0.16
indel+null 508 2,526,058,354 2.01e-07 0.20 0.18
double_null 5 2,526,058,354 1.98e-09 0.0020 0.0017
Total 2882 2,526,058,354 1.14e-06 1.14 1.00

category	n	N	rate	rate_per_mb	relative_rate
A->T	610	1,231,130,036	4.95e-07	0.50	0.43
C->(A/T)	898	1,294,928,235	6.93e-07	0.69	0.61
A->(C/G)	622	1,231,130,036	5.05e-07	0.51	0.44
C->G	239	1,294,928,235	1.85e-07	0.18	0.16
indel+null	508	2,526,058,354	2.01e-07	0.20	0.18
double_null	5	2,526,058,354	1.98e-09	0.0020	0.0017
Total	2882	2,526,058,354	1.14e-06	1.14	1.00

Target coverage for each individual

(click for higher-resolution version)

Mutation counts, total coverage, and mutation rates for each individual

(click for higher-resolution version)
(click for tabular version)

Significantly mutated genes

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 NKX3-1 NK3 homeobox 1 50049 5 5 5 0 0 0 4 0 1 0 3.23e-11 5.83e-07
2 MUC4 mucin 4, cell surface associated 541492 11 10 7 1 4 2 5 0 0 0 2.74e-10 2.47e-06
3 FRG1 FSHD region gene 1 67479 6 5 4 0 3 1 1 0 1 0 1.22e-09 7.36e-06
4 SCAI 158447 5 5 2 0 0 4 0 1 0 0 2.62e-07 0.0012
5 PRIM2 primase, DNA, polypeptide 2 (58kDa) 124915 4 4 2 4 0 1 0 0 3 0 4.41e-07 0.0014
6 C9orf150 chromosome 9 open reading frame 150 48721 3 3 1 0 0 0 0 0 3 0 4.78e-07 0.0014
7 CDC27 cell division cycle 27 homolog (S. cerevisiae) 213227 6 5 6 6 0 5 0 0 1 0 6.72e-07 0.0017
8 SPOP speckle-type POZ protein 96363 4 4 3 0 0 0 4 0 0 0 8.62e-07 0.0019
9 ZNF98 zinc finger protein 98 (F7175) 143507 4 4 4 0 0 1 1 1 1 0 1.80e-06 0.0036
10 LILRB3 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3 121678 4 4 2 0 0 0 4 0 0 0 3.01e-06 0.0054
11 TP53 tumor protein p53 106406 4 4 4 0 1 2 0 0 1 0 3.35e-06 0.0055
12 SLITRK4 SLIT and NTRK-like family, member 4 208994 3 3 2 0 0 0 0 0 3 0 9.34e-06 0.014
13 LRIT2 leucine-rich repeat, immunoglobulin-like and transmembrane domains 2 138195 4 4 3 0 2 2 0 0 0 0 0.000013 0.017
14 FCGBP Fc fragment of IgG binding protein 979151 7 7 5 1 1 1 4 1 0 0 0.000013 0.017
15 NOTCH2NL Notch homolog 2 (Drosophila) N-terminal like 60341 3 3 2 0 0 1 2 0 0 0 0.000015 0.018
16 PDE4DIP phosphodiesterase 4D interacting protein (myomegalin) 344367 5 5 4 1 1 0 3 0 1 0 0.000018 0.020
17 ZNF492 zinc finger protein 492 133464 4 4 3 0 3 1 0 0 0 0 0.000019 0.020
18 ZNF99 zinc finger protein 99 260869 4 4 4 3 0 1 1 1 1 0 0.000020 0.020
19 ETV3 ets variant gene 3 36852 2 2 2 0 0 0 1 0 1 0 0.000025 0.024
20 TPTE2 transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 136867 3 3 3 0 0 1 1 0 1 0 0.000032 0.028
21 TTLL11 tubulin tyrosine ligase-like family, member 11 84079 3 3 3 0 0 2 0 0 1 0 0.000033 0.028
22 PRR21 55859 3 3 3 0 1 1 1 0 0 0 0.000035 0.028
23 FIP1L1 FIP1 like 1 (S. cerevisiae) 156704 3 3 1 0 0 0 0 0 3 0 0.000036 0.028
24 AIM2 absent in melanoma 2 87316 3 3 3 0 0 1 0 1 1 0 0.000044 0.033
25 CROCC ciliary rootlet coiled-coil, rootletin 319965 4 4 2 1 0 4 0 0 0 0 0.000048 0.035
26 BBS9 Bardet-Biedl syndrome 9 228416 3 3 2 0 0 0 1 0 2 0 0.000059 0.041
27 CTNNAL1 catenin (cadherin-associated protein), alpha-like 1 177288 3 3 2 0 0 1 0 0 2 0 0.000063 0.042
28 OR6N1 olfactory receptor, family 6, subfamily N, member 1 78269 3 3 2 0 1 0 0 2 0 0 0.000075 0.049
29 ATF7IP activating transcription factor 7 interacting protein 321127 3 3 3 0 0 0 2 0 1 0 0.00010 0.064
30 CRIPAK cysteine-rich PAK1 inhibitor 111552 3 3 3 1 1 1 1 0 0 0 0.00011 0.066

(click for full table with 18033 genes)

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	NKX3-1	NK3 homeobox 1	50049	5	5	5	0	0	0	4	0	1	3.23e-11	5.83e-07
2	MUC4	mucin 4, cell surface associated	541492	11	10	7	1	4	2	5	0	0	2.74e-10	2.47e-06
3	FRG1	FSHD region gene 1	67479	6	5	4	0	3	1	1	0	1	1.22e-09	7.36e-06
4	SCAI		158447	5	5	2	0	0	4	0	1	0	2.62e-07	0.0012
5	PRIM2	primase, DNA, polypeptide 2 (58kDa)	124915	4	4	2	4	0	1	0	0	3	4.41e-07	0.0014
6	C9orf150	chromosome 9 open reading frame 150	48721	3	3	1	0	0	0	0	0	3	4.78e-07	0.0014
7	CDC27	cell division cycle 27 homolog (S. cerevisiae)	213227	6	5	6	6	0	5	0	0	1	6.72e-07	0.0017
8	SPOP	speckle-type POZ protein	96363	4	4	3	0	0	0	4	0	0	8.62e-07	0.0019
9	ZNF98	zinc finger protein 98 (F7175)	143507	4	4	4	0	0	1	1	1	1	1.80e-06	0.0036
10	LILRB3	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	121678	4	4	2	0	0	0	4	0	0	3.01e-06	0.0054
11	TP53	tumor protein p53	106406	4	4	4	0	1	2	0	0	1	3.35e-06	0.0055
12	SLITRK4	SLIT and NTRK-like family, member 4	208994	3	3	2	0	0	0	0	0	3	9.34e-06	0.014
13	LRIT2	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	138195	4	4	3	0	2	2	0	0	0	0.000013	0.017
14	FCGBP	Fc fragment of IgG binding protein	979151	7	7	5	1	1	1	4	1	0	0.000013	0.017
15	NOTCH2NL	Notch homolog 2 (Drosophila) N-terminal like	60341	3	3	2	0	0	1	2	0	0	0.000015	0.018
16	PDE4DIP	phosphodiesterase 4D interacting protein (myomegalin)	344367	5	5	4	1	1	0	3	0	1	0.000018	0.020
17	ZNF492	zinc finger protein 492	133464	4	4	3	0	3	1	0	0	0	0.000019	0.020
18	ZNF99	zinc finger protein 99	260869	4	4	4	3	0	1	1	1	1	0.000020	0.020
19	ETV3	ets variant gene 3	36852	2	2	2	0	0	0	1	0	1	0.000025	0.024
20	TPTE2	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	136867	3	3	3	0	0	1	1	0	1	0.000032	0.028
21	TTLL11	tubulin tyrosine ligase-like family, member 11	84079	3	3	3	0	0	2	0	0	1	0.000033	0.028
22	PRR21		55859	3	3	3	0	1	1	1	0	0	0.000035	0.028
23	FIP1L1	FIP1 like 1 (S. cerevisiae)	156704	3	3	1	0	0	0	0	0	3	0.000036	0.028
24	AIM2	absent in melanoma 2	87316	3	3	3	0	0	1	0	1	1	0.000044	0.033
25	CROCC	ciliary rootlet coiled-coil, rootletin	319965	4	4	2	1	0	4	0	0	0	0.000048	0.035
26	BBS9	Bardet-Biedl syndrome 9	228416	3	3	2	0	0	0	1	0	2	0.000059	0.041
27	CTNNAL1	catenin (cadherin-associated protein), alpha-like 1	177288	3	3	2	0	0	1	0	0	2	0.000063	0.042
28	OR6N1	olfactory receptor, family 6, subfamily N, member 1	78269	3	3	2	0	1	0	0	2	0	0.000075	0.049
29	ATF7IP	activating transcription factor 7 interacting protein	321127	3	3	3	0	0	0	2	0	1	0.00010	0.064
30	CRIPAK	cysteine-rich PAK1 inhibitor	111552	3	3	3	1	1	1	1	0	0	0.00011	0.066

Notes
N = number of sequenced bases in this gene across the individual set
n = number of (nonsilent) mutations in this gene across the individual set
npat = number of patients (individuals) with at least one nonsilent mutation
nsite = number of unique sites having a nonsilent mutation
nsil = number of silent mutations in this gene across the individual set
n1 = number of nonsilent mutations of type "A->T"
n2 = number of nonsilent mutations of type "C->(A/T)"
n3 = number of nonsilent mutations of type "A->(C/G)"
n4 = number of nonsilent mutations of type "C->G"
n5 = number of nonsilent mutations of type "indel+null"
n6 = number of nonsilent mutations of type "double_null"
null = mutation category that includes nonsense, frameshift, splice-site mutations
p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
p_ks = p-value for clustering of mutations (Kolmogorov-Smirnoff test)
p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene
p_joint = p-value for clustering + conservation
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Gene-gene correlations / anti-correlations

gene1 gene2 p q relationship
MUC4 RNF17 0.0018 0.91 correlated
ATF7IP FCGBP 0.0029 0.91 correlated
TTLL11 ZNF99 0.0071 0.93 correlated
LRIT2 MUC4 0.0081 0.93 correlated
LRIT2 RNF17 0.030 0.93 correlated
MUC4 PDE4DIP 0.034 0.93 correlated
CDC27 LILRB3 0.045 0.93 correlated
MUC4 TP53 0.069 0.93 none
ETV3 PIP5K1C 0.071 0.93 none
BBS9 ETV3 0.071 0.93 none
NOTCH2NL TAL2 0.071 0.93 none
TAL2 ZNF492 0.095 0.93 none
AIM2 CRIPAK 0.11 0.93 none
AIM2 OR6N1 0.11 0.93 none
AIM2 RNF17 0.11 0.93 none
ATF7IP SLITRK4 0.11 0.93 none
BBS9 KRT25 0.11 0.93 none
BBS9 NOTCH2NL 0.11 0.93 none
BBS9 PIP5K1C 0.11 0.93 none
BBS9 TPTE2 0.11 0.93 none
C9orf150 PRR21 0.11 0.93 none
CRIPAK CTNNAL1 0.11 0.93 none
CRIPAK RNF17 0.11 0.93 none
CRIPAK SLITRK4 0.11 0.93 none
CTNNAL1 ESCO1 0.11 0.93 none
CTNNAL1 RCBTB2 0.11 0.93 none
CTNNAL1 SLITRK4 0.11 0.93 none
ESCO1 RCBTB2 0.11 0.93 none
ESCO1 SLITRK4 0.11 0.93 none
FIP1L1 RNF17 0.11 0.93 none

(click for full table with 630 gene-gene pairs)

gene1	gene2	p	q	relationship
MUC4	RNF17	0.0018	0.91	correlated
ATF7IP	FCGBP	0.0029	0.91	correlated
TTLL11	ZNF99	0.0071	0.93	correlated
LRIT2	MUC4	0.0081	0.93	correlated
LRIT2	RNF17	0.030	0.93	correlated
MUC4	PDE4DIP	0.034	0.93	correlated
CDC27	LILRB3	0.045	0.93	correlated
MUC4	TP53	0.069	0.93	none
ETV3	PIP5K1C	0.071	0.93	none
BBS9	ETV3	0.071	0.93	none
NOTCH2NL	TAL2	0.071	0.93	none
TAL2	ZNF492	0.095	0.93	none
AIM2	CRIPAK	0.11	0.93	none
AIM2	OR6N1	0.11	0.93	none
AIM2	RNF17	0.11	0.93	none
ATF7IP	SLITRK4	0.11	0.93	none
BBS9	KRT25	0.11	0.93	none
BBS9	NOTCH2NL	0.11	0.93	none
BBS9	PIP5K1C	0.11	0.93	none
BBS9	TPTE2	0.11	0.93	none
C9orf150	PRR21	0.11	0.93	none
CRIPAK	CTNNAL1	0.11	0.93	none
CRIPAK	RNF17	0.11	0.93	none
CRIPAK	SLITRK4	0.11	0.93	none
CTNNAL1	ESCO1	0.11	0.93	none
CTNNAL1	RCBTB2	0.11	0.93	none
CTNNAL1	SLITRK4	0.11	0.93	none
ESCO1	RCBTB2	0.11	0.93	none
ESCO1	SLITRK4	0.11	0.93	none
FIP1L1	RNF17	0.11	0.93	none

Notes
p = probability of obtaining the observed degree of correlation or anti-correlation
between the given pair of genes, calculated by performing many random permutations of the
gene labels on the mutations in the dataset, thereby controling for sample-specific
and gene-specific mutation rates.
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure), correcting for the
multiple hypotheses (one hypothesis per pair of genes considered.)

COSMIC analyses

Two distinct analyses are reported using the COSMIC database:
(COS1) COSMIC used as a filter to increase power by restricting the territory of each gene
(COS2) COSMIC used as a prior for the importance of a gene

(COS1) Significantly mutated genes (COSMIC territory only)

rank gene description n cos n_cos N_cos cos_ev p q

(click for full table with 4520 genes)

Notes
n = number of mutations in this gene in the individual set
cos = number of unique mutated sites in this gene in COSMIC
n_cos = overlap between n and cos
N_cos = number of individuals × cos
cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene
p = p-value for seeing the observed amount of overlap in this gene
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

(COS2) Genes mutated at sites that are highly reported in COSMIC

rank gene description n cos n_cos cos_ev

(click for full table with 4520 genes)

Notes
n = number of mutations in this gene in the individual set
cos = number of unique mutated sites in this gene in COSMIC
n_cos = overlap between n and cos
cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene

Mutations reported in COSMIC

patient chr start end type gene Protein_Change n_cos

(click for full table with 0 mutations)

Genes with clustered mutations

rank gene desc n mindist npairs3 npairs12
1 FANCD2 Fanconi anemia, complementation group D2 2 0 1 1
2 A2BP1 2 Inf 0 0
3 ABCA4 ATP-binding cassette, sub-family A (ABC1), member 4 2 Inf 0 0
4 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 2 Inf 0 0
5 ABCC11 ATP-binding cassette, sub-family C (CFTR/MRP), member 11 2 Inf 0 0
6 ACAN aggrecan 2 Inf 0 0
7 ADAM29 ADAM metallopeptidase domain 29 2 Inf 0 0
8 ADAMTS13 ADAM metallopeptidase with thrombospondin type 1 motif, 13 2 Inf 0 0
9 ADAMTSL1 ADAMTS-like 1 2 Inf 0 0
10 ADNP activity-dependent neuroprotector homeobox 2 Inf 0 0
11 AFG3L2 AFG3 ATPase family gene 3-like 2 (yeast) 2 Inf 0 0
12 AHNAK2 AHNAK nucleoprotein 2 4 Inf 0 0
13 AIM2 absent in melanoma 2 3 Inf 0 0
14 ANK3 ankyrin 3, node of Ranvier (ankyrin G) 2 Inf 0 0
15 ANKRD56 ankyrin repeat domain 56 2 Inf 0 0
16 ANLN anillin, actin binding protein 2 Inf 0 0
17 ANO4 2 Inf 0 0
18 AP3B2 adaptor-related protein complex 3, beta 2 subunit 3 Inf 0 0
19 AP4B1 adaptor-related protein complex 4, beta 1 subunit 2 Inf 0 0
20 APOB apolipoprotein B (including Ag(x) antigen) 2 Inf 0 0
21 ARHGAP21 Rho GTPase activating protein 21 2 Inf 0 0
22 ARHGAP30 Rho GTPase activating protein 30 2 Inf 0 0
23 ARHGEF10 Rho guanine nucleotide exchange factor (GEF) 10 2 Inf 0 0
24 ARID2 AT rich interactive domain 2 (ARID, RFX-like) 2 Inf 0 0
25 ARID4B AT rich interactive domain 4B (RBP1-like) 2 Inf 0 0
26 ASB2 ankyrin repeat and SOCS box-containing 2 2 Inf 0 0
27 ASH1L ash1 (absent, small, or homeotic)-like (Drosophila) 4 Inf 0 0
28 ASTN1 astrotactin 1 2 Inf 0 0
29 ATAD2 ATPase family, AAA domain containing 2 2 Inf 0 0
30 ATF7IP activating transcription factor 7 interacting protein 3 Inf 0 0

(click for full table with 2321 genes)

rank	gene	desc	n	mindist	npairs3	npairs12
1	FANCD2	Fanconi anemia, complementation group D2	2	0	1	1
2	A2BP1		2	Inf	0	0
3	ABCA4	ATP-binding cassette, sub-family A (ABC1), member 4	2	Inf	0	0
4	ABCB1	ATP-binding cassette, sub-family B (MDR/TAP), member 1	2	Inf	0	0
5	ABCC11	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	2	Inf	0	0
6	ACAN	aggrecan	2	Inf	0	0
7	ADAM29	ADAM metallopeptidase domain 29	2	Inf	0	0
8	ADAMTS13	ADAM metallopeptidase with thrombospondin type 1 motif, 13	2	Inf	0	0
9	ADAMTSL1	ADAMTS-like 1	2	Inf	0	0
10	ADNP	activity-dependent neuroprotector homeobox	2	Inf	0	0
11	AFG3L2	AFG3 ATPase family gene 3-like 2 (yeast)	2	Inf	0	0
12	AHNAK2	AHNAK nucleoprotein 2	4	Inf	0	0
13	AIM2	absent in melanoma 2	3	Inf	0	0
14	ANK3	ankyrin 3, node of Ranvier (ankyrin G)	2	Inf	0	0
15	ANKRD56	ankyrin repeat domain 56	2	Inf	0	0
16	ANLN	anillin, actin binding protein	2	Inf	0	0
17	ANO4		2	Inf	0	0
18	AP3B2	adaptor-related protein complex 3, beta 2 subunit	3	Inf	0	0
19	AP4B1	adaptor-related protein complex 4, beta 1 subunit	2	Inf	0	0
20	APOB	apolipoprotein B (including Ag(x) antigen)	2	Inf	0	0
21	ARHGAP21	Rho GTPase activating protein 21	2	Inf	0	0
22	ARHGAP30	Rho GTPase activating protein 30	2	Inf	0	0
23	ARHGEF10	Rho guanine nucleotide exchange factor (GEF) 10	2	Inf	0	0
24	ARID2	AT rich interactive domain 2 (ARID, RFX-like)	2	Inf	0	0
25	ARID4B	AT rich interactive domain 4B (RBP1-like)	2	Inf	0	0
26	ASB2	ankyrin repeat and SOCS box-containing 2	2	Inf	0	0
27	ASH1L	ash1 (absent, small, or homeotic)-like (Drosophila)	4	Inf	0	0
28	ASTN1	astrotactin 1	2	Inf	0	0
29	ATAD2	ATPase family, AAA domain containing 2	2	Inf	0	0
30	ATF7IP	activating transcription factor 7 interacting protein	3	Inf	0	0

Notes
n = number of mutations in this gene in the individual set
mindist = distance (in aa) between closest pair of mutations in this gene
npairs3 = how many pairs of mutations are within 3 aa of each other
npairs12 = how many pairs of mutations are within 12 aa of each other

Significantly mutated genesets

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 HSA04310_WNT_SIGNALING_ PATHWAY Genes involved in Wnt signaling pathway APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B 144 CACYBP(1), CHP(1), CSNK1A1L(1), CTNNB1(3), DAAM2(2), DKK2(1), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), LEF1(1), LRP6(1), PPARD(1), PPP2R2B(1), PPP2R2C(1), PRICKLE2(1), PSEN1(1), RAC1(1), ROCK1(1), SFRP2(1), SMAD3(1), SOX17(1), TBL1XR1(2), TCF7L2(1), TP53(4), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1) 20782868 46 34 45 17 7 17 7 3 12 0 5.72e-08 0.000035
2 SA_G1_AND_S_PHASES Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53 15 CDKN1B(2), PRB1(2), TP53(4) 1017580 8 8 8 0 1 2 2 0 3 0 5.10e-06 0.0016
3 WNT_SIGNALING Wnt signaling genes APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B 58 CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD5(1), FZD6(1), FZD9(1), LDLR(1), PLAU(1), PPP2R5E(1), RAC1(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1) 7614586 22 17 21 6 3 6 4 4 5 0 0.000018 0.0036
4 SA_REG_CASCADE_OF_ CYCLIN_EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1 13 CCNA1(1), CCNE2(1), CDKN1B(2), PRB1(2) 1096762 6 6 6 0 1 0 3 0 2 0 0.00050 0.072
5 PLK3PATHWAY Active Plk3 phosphorylates CDC25c, blocking the G2/M transition, and phosphorylates p53 to induce apoptosis. ATM, ATR, CDC25C, CHEK1, CHEK2, CNK, TP53, YWHAH 7 ATM(2), CHEK2(2), TP53(4) 2002126 8 8 7 0 1 3 1 2 1 0 0.00059 0.072
6 HSA04916_MELANOGENESIS Genes involved in melanogenesis ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ASIP, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CREB1, CREB3, CREB3L1, CREB3L2, CREB3L3, CREB3L4, CREBBP, CTNNB1, DCT, DVL1, DVL2, DVL3, EDN1, EDNRB, EP300, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GSK3B, HRAS, KIT, KITLG, KRAS, LEF1, LOC652788, MAP2K1, MAP2K2, MAPK1, MAPK3, MC1R, MITF, NRAS, PLCB1, PLCB2, PLCB3, PLCB4, POMC, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, RAF1, TCF7, TCF7L1, TCF7L2, TYR, TYRP1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B 99 ADCY6(1), ADCY9(1), CALML6(1), CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), GNAQ(1), LEF1(1), TCF7L2(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1) 13939850 27 21 26 15 5 9 3 3 7 0 0.00081 0.083
7 HSA00564_GLYCEROPHOSPHOLIPID_ METABOLISM Genes involved in glycerophospholipid metabolism ACHE, AGPAT1, AGPAT2, AGPAT3, AGPAT4, AGPAT6, ARD1A, CDIPT, CDS1, CDS2, CHAT, CHKA, CHKB, CHPT1, CRLS1, DGKA, DGKB, DGKD, DGKE, DGKG, DGKH, DGKI, DGKQ, DGKZ, ESCO1, ESCO2, ETNK1, ETNK2, GNPAT, GPAM, GPD1, GPD1L, GPD2, LCAT, LYCAT, LYPLA1, LYPLA2, LYPLA3, MYST3, MYST4, NAT5, NAT6, PCYT1A, PCYT1B, PEMT, PHOSPHO1, PISD, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLD1, PLD2, PNPLA3, PPAP2A, PPAP2B, PPAP2C, PTDSS1, PTDSS2, SH3GLB1 64 AGPAT2(1), AGPAT3(1), DGKD(1), DGKI(1), DGKQ(2), ESCO1(3), GNPAT(1), MYST3(1), PLA2G2A(1), PLA2G4A(1), PLA2G5(1), PLD1(1), PTDSS1(1) 8437614 16 15 16 2 2 3 4 3 4 0 0.0012 0.10
8 STAT3PATHWAY The STAT transcription factors are phosphorylated and activated by JAK kinases in response to cytokine signaling. FRAP1, JAK1, JAK2, JAK3, MAPK1, MAPK3, STAT3, TYK2 7 JAK1(3), STAT3(2), TYK2(1) 1521473 6 5 6 1 1 1 1 1 2 0 0.0013 0.10
9 P53HYPOXIAPATHWAY Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage. ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53 19 ABCB1(2), AKT1(1), ATM(2), TP53(4) 2646704 9 9 9 0 2 4 1 1 1 0 0.0021 0.14
10 G1PATHWAY CDK4/6-cyclin D and CDK2-cyclin E phosphorylate Rb, which allows the transcription of genes needed for the G1/S cell cycle transition. ABL1, ATM, ATR, CCNA1, CCND1, CCNE1, CDC2, CDC25A, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, DHFR, E2F1, GSK3B, HDAC1, MADH3, MADH4, RB1, SKP2, TFDP1, TGFB1, TGFB2, TGFB3, TP53 25 ATM(2), CCNA1(1), CDKN1B(2), DHFR(1), TP53(4) 3767619 10 10 10 0 2 3 1 0 4 0 0.0025 0.15

(click for full table with 616 genesets)

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	HSA04310_WNT_SIGNALING_ PATHWAY	Genes involved in Wnt signaling pathway	APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B	144	CACYBP(1), CHP(1), CSNK1A1L(1), CTNNB1(3), DAAM2(2), DKK2(1), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), LEF1(1), LRP6(1), PPARD(1), PPP2R2B(1), PPP2R2C(1), PRICKLE2(1), PSEN1(1), RAC1(1), ROCK1(1), SFRP2(1), SMAD3(1), SOX17(1), TBL1XR1(2), TCF7L2(1), TP53(4), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1)	20782868	46	34	45	17	7	17	7	3	12	5.72e-08	0.000035
2	SA_G1_AND_S_PHASES	Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition.	ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53	15	CDKN1B(2), PRB1(2), TP53(4)	1017580	8	8	8	0	1	2	2	0	3	5.10e-06	0.0016
3	WNT_SIGNALING	Wnt signaling genes	APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B	58	CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD5(1), FZD6(1), FZD9(1), LDLR(1), PLAU(1), PPP2R5E(1), RAC1(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1)	7614586	22	17	21	6	3	6	4	4	5	0.000018	0.0036
4	SA_REG_CASCADE_OF_ CYCLIN_EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.	CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1	13	CCNA1(1), CCNE2(1), CDKN1B(2), PRB1(2)	1096762	6	6	6	0	1	0	3	0	2	0.00050	0.072
5	PLK3PATHWAY	Active Plk3 phosphorylates CDC25c, blocking the G2/M transition, and phosphorylates p53 to induce apoptosis.	ATM, ATR, CDC25C, CHEK1, CHEK2, CNK, TP53, YWHAH	7	ATM(2), CHEK2(2), TP53(4)	2002126	8	8	7	0	1	3	1	2	1	0.00059	0.072
6	HSA04916_MELANOGENESIS	Genes involved in melanogenesis	ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ASIP, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CREB1, CREB3, CREB3L1, CREB3L2, CREB3L3, CREB3L4, CREBBP, CTNNB1, DCT, DVL1, DVL2, DVL3, EDN1, EDNRB, EP300, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GSK3B, HRAS, KIT, KITLG, KRAS, LEF1, LOC652788, MAP2K1, MAP2K2, MAPK1, MAPK3, MC1R, MITF, NRAS, PLCB1, PLCB2, PLCB3, PLCB4, POMC, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, RAF1, TCF7, TCF7L1, TCF7L2, TYR, TYRP1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B	99	ADCY6(1), ADCY9(1), CALML6(1), CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), GNAQ(1), LEF1(1), TCF7L2(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1)	13939850	27	21	26	15	5	9	3	3	7	0.00081	0.083
7	HSA00564_GLYCEROPHOSPHOLIPID_ METABOLISM	Genes involved in glycerophospholipid metabolism	ACHE, AGPAT1, AGPAT2, AGPAT3, AGPAT4, AGPAT6, ARD1A, CDIPT, CDS1, CDS2, CHAT, CHKA, CHKB, CHPT1, CRLS1, DGKA, DGKB, DGKD, DGKE, DGKG, DGKH, DGKI, DGKQ, DGKZ, ESCO1, ESCO2, ETNK1, ETNK2, GNPAT, GPAM, GPD1, GPD1L, GPD2, LCAT, LYCAT, LYPLA1, LYPLA2, LYPLA3, MYST3, MYST4, NAT5, NAT6, PCYT1A, PCYT1B, PEMT, PHOSPHO1, PISD, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLD1, PLD2, PNPLA3, PPAP2A, PPAP2B, PPAP2C, PTDSS1, PTDSS2, SH3GLB1	64	AGPAT2(1), AGPAT3(1), DGKD(1), DGKI(1), DGKQ(2), ESCO1(3), GNPAT(1), MYST3(1), PLA2G2A(1), PLA2G4A(1), PLA2G5(1), PLD1(1), PTDSS1(1)	8437614	16	15	16	2	2	3	4	3	4	0.0012	0.10
8	STAT3PATHWAY	The STAT transcription factors are phosphorylated and activated by JAK kinases in response to cytokine signaling.	FRAP1, JAK1, JAK2, JAK3, MAPK1, MAPK3, STAT3, TYK2	7	JAK1(3), STAT3(2), TYK2(1)	1521473	6	5	6	1	1	1	1	1	2	0.0013	0.10
9	P53HYPOXIAPATHWAY	Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage.	ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53	19	ABCB1(2), AKT1(1), ATM(2), TP53(4)	2646704	9	9	9	0	2	4	1	1	1	0.0021	0.14
10	G1PATHWAY	CDK4/6-cyclin D and CDK2-cyclin E phosphorylate Rb, which allows the transcription of genes needed for the G1/S cell cycle transition.	ABL1, ATM, ATR, CCNA1, CCND1, CCNE1, CDC2, CDC25A, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, DHFR, E2F1, GSK3B, HDAC1, MADH3, MADH4, RB1, SKP2, TFDP1, TGFB1, TGFB2, TGFB3, TP53	25	ATM(2), CCNA1(1), CDKN1B(2), DHFR(1), TP53(4)	3767619	10	10	10	0	2	3	1	0	4	0.0025	0.15

Notes: (Please see notes under significantly mutated gene table)

Significantly mutated genesets (excluding significantly mutated genes)

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 HSA04310_WNT_SIGNALING_ PATHWAY Genes involved in Wnt signaling pathway APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B 143 CACYBP(1), CHP(1), CSNK1A1L(1), CTNNB1(3), DAAM2(2), DKK2(1), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), LEF1(1), LRP6(1), PPARD(1), PPP2R2B(1), PPP2R2C(1), PRICKLE2(1), PSEN1(1), RAC1(1), ROCK1(1), SFRP2(1), SMAD3(1), SOX17(1), TBL1XR1(2), TCF7L2(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1) 20676462 42 32 41 17 6 15 7 3 11 0 4.64e-07 0.00029
2 WNT_SIGNALING Wnt signaling genes APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B 58 CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD5(1), FZD6(1), FZD9(1), LDLR(1), PLAU(1), PPP2R5E(1), RAC1(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1) 7614586 22 17 21 6 3 6 4 4 5 0 0.000018 0.0055
3 SA_REG_CASCADE_OF_ CYCLIN_EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1 13 CCNA1(1), CCNE2(1), CDKN1B(2), PRB1(2) 1096762 6 6 6 0 1 0 3 0 2 0 0.00050 0.10
4 HSA04916_MELANOGENESIS Genes involved in melanogenesis ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ASIP, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CREB1, CREB3, CREB3L1, CREB3L2, CREB3L3, CREB3L4, CREBBP, CTNNB1, DCT, DVL1, DVL2, DVL3, EDN1, EDNRB, EP300, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GSK3B, HRAS, KIT, KITLG, KRAS, LEF1, LOC652788, MAP2K1, MAP2K2, MAPK1, MAPK3, MC1R, MITF, NRAS, PLCB1, PLCB2, PLCB3, PLCB4, POMC, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, RAF1, TCF7, TCF7L1, TCF7L2, TYR, TYRP1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B 99 ADCY6(1), ADCY9(1), CALML6(1), CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), GNAQ(1), LEF1(1), TCF7L2(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1) 13939850 27 21 26 15 5 9 3 3 7 0 0.00081 0.12
5 STAT3PATHWAY The STAT transcription factors are phosphorylated and activated by JAK kinases in response to cytokine signaling. FRAP1, JAK1, JAK2, JAK3, MAPK1, MAPK3, STAT3, TYK2 7 JAK1(3), STAT3(2), TYK2(1) 1521473 6 5 6 1 1 1 1 1 2 0 0.0013 0.16
6 HSA00830_RETINOL_ METABOLISM Genes involved in retinol metabolism ALDH1A1, ALDH1A2, BCMO1, RDH5 4 ALDH1A2(1), BCMO1(2) 483724 3 3 2 0 0 0 1 2 0 0 0.0030 0.30
7 HSA04080_NEUROACTIVE_ LIGAND_RECEPTOR_ INTERACTION Genes involved in neuroactive ligand-receptor interaction ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2 237 ADRA2A(1), AGTR1(1), AVPR1A(1), CHRM4(1), DRD5(1), GABRE(2), GABRG1(2), GABRQ(1), GABRR1(1), GABRR2(2), GHR(1), GLP2R(1), GLRA2(1), GRIA1(1), GRIA4(1), GRID1(1), GRID2(3), GRIK1(1), GRIK4(1), GRIN2A(1), GRIN3B(1), GRM1(1), GRM4(1), GRM5(2), GRM7(2), GZMA(1), HTR5A(1), MTNR1A(1), P2RX5(1), P2RY1(1), PRSS3(1), PTGER2(1), RXFP1(1), SSTR2(1), TACR3(1), TBXA2R(1) 28288807 43 36 42 14 15 17 1 3 7 0 0.0046 0.36
8 STRIATED_MUSCLE_ CONTRACTION ACTA1, ACTA2, ACTC, ACTN2, ACTN3, ACTN4, C9orf97, DES, DES, FAM48A, DMD, MYBPC1, MYBPC2, MYBPC3, MYH3, MYH6, MYH6, MYH7, MYH8, MYL1, MYL2, MYL3, MYL4, MYL9, MYOM1, NEB, TCAP, TMOD1, TNNC2, TNNI1, TNNI2, TNNI3, TNNT1, TNNT2, TNNT3, TPM1, TPM2, TPM3, TPM4, TPM4, TTN, VIM 37 DMD(1), MYBPC1(1), MYBPC2(1), MYBPC3(1), MYH6(2), MYH7(1), MYH8(1), MYL1(1), NEB(2), TTN(18) 17519972 29 27 28 1 7 8 5 5 4 0 0.0047 0.36
9 SA_G1_AND_S_PHASES Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53 14 CDKN1B(2), PRB1(2) 911174 4 4 4 0 0 0 2 0 2 0 0.0053 0.36
10 SMALL_LIGAND_GPCRS C9orf47, CNR1, CNR2, DNMT1, EDG1, EDG2, EDG5, EDG6, MTNR1A, MTNR1B, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, TBXA2R 14 DNMT1(2), MTNR1A(1), PTGER2(1), TBXA2R(1) 1476736 5 5 5 0 0 2 0 2 1 0 0.0063 0.36

(click for full table with 616 genesets)

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	HSA04310_WNT_SIGNALING_ PATHWAY	Genes involved in Wnt signaling pathway	APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B	143	CACYBP(1), CHP(1), CSNK1A1L(1), CTNNB1(3), DAAM2(2), DKK2(1), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), LEF1(1), LRP6(1), PPARD(1), PPP2R2B(1), PPP2R2C(1), PRICKLE2(1), PSEN1(1), RAC1(1), ROCK1(1), SFRP2(1), SMAD3(1), SOX17(1), TBL1XR1(2), TCF7L2(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1)	20676462	42	32	41	17	6	15	7	3	11	4.64e-07	0.00029
2	WNT_SIGNALING	Wnt signaling genes	APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B	58	CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD5(1), FZD6(1), FZD9(1), LDLR(1), PLAU(1), PPP2R5E(1), RAC1(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1)	7614586	22	17	21	6	3	6	4	4	5	0.000018	0.0055
3	SA_REG_CASCADE_OF_ CYCLIN_EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.	CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1	13	CCNA1(1), CCNE2(1), CDKN1B(2), PRB1(2)	1096762	6	6	6	0	1	0	3	0	2	0.00050	0.10
4	HSA04916_MELANOGENESIS	Genes involved in melanogenesis	ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ASIP, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CREB1, CREB3, CREB3L1, CREB3L2, CREB3L3, CREB3L4, CREBBP, CTNNB1, DCT, DVL1, DVL2, DVL3, EDN1, EDNRB, EP300, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GSK3B, HRAS, KIT, KITLG, KRAS, LEF1, LOC652788, MAP2K1, MAP2K2, MAPK1, MAPK3, MC1R, MITF, NRAS, PLCB1, PLCB2, PLCB3, PLCB4, POMC, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, RAF1, TCF7, TCF7L1, TCF7L2, TYR, TYRP1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B	99	ADCY6(1), ADCY9(1), CALML6(1), CTNNB1(3), DVL2(1), FZD1(1), FZD2(4), FZD4(2), FZD5(1), FZD6(1), FZD9(1), GNAQ(1), LEF1(1), TCF7L2(1), WNT1(1), WNT10B(1), WNT11(2), WNT2(1), WNT5A(1), WNT9A(1)	13939850	27	21	26	15	5	9	3	3	7	0.00081	0.12
5	STAT3PATHWAY	The STAT transcription factors are phosphorylated and activated by JAK kinases in response to cytokine signaling.	FRAP1, JAK1, JAK2, JAK3, MAPK1, MAPK3, STAT3, TYK2	7	JAK1(3), STAT3(2), TYK2(1)	1521473	6	5	6	1	1	1	1	1	2	0.0013	0.16
6	HSA00830_RETINOL_ METABOLISM	Genes involved in retinol metabolism	ALDH1A1, ALDH1A2, BCMO1, RDH5	4	ALDH1A2(1), BCMO1(2)	483724	3	3	2	0	0	0	1	2	0	0.0030	0.30
7	HSA04080_NEUROACTIVE_ LIGAND_RECEPTOR_ INTERACTION	Genes involved in neuroactive ligand-receptor interaction	ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2	237	ADRA2A(1), AGTR1(1), AVPR1A(1), CHRM4(1), DRD5(1), GABRE(2), GABRG1(2), GABRQ(1), GABRR1(1), GABRR2(2), GHR(1), GLP2R(1), GLRA2(1), GRIA1(1), GRIA4(1), GRID1(1), GRID2(3), GRIK1(1), GRIK4(1), GRIN2A(1), GRIN3B(1), GRM1(1), GRM4(1), GRM5(2), GRM7(2), GZMA(1), HTR5A(1), MTNR1A(1), P2RX5(1), P2RY1(1), PRSS3(1), PTGER2(1), RXFP1(1), SSTR2(1), TACR3(1), TBXA2R(1)	28288807	43	36	42	14	15	17	1	3	7	0.0046	0.36
8	STRIATED_MUSCLE_ CONTRACTION		ACTA1, ACTA2, ACTC, ACTN2, ACTN3, ACTN4, C9orf97, DES, DES, FAM48A, DMD, MYBPC1, MYBPC2, MYBPC3, MYH3, MYH6, MYH6, MYH7, MYH8, MYL1, MYL2, MYL3, MYL4, MYL9, MYOM1, NEB, TCAP, TMOD1, TNNC2, TNNI1, TNNI2, TNNI3, TNNT1, TNNT2, TNNT3, TPM1, TPM2, TPM3, TPM4, TPM4, TTN, VIM	37	DMD(1), MYBPC1(1), MYBPC2(1), MYBPC3(1), MYH6(2), MYH7(1), MYH8(1), MYL1(1), NEB(2), TTN(18)	17519972	29	27	28	1	7	8	5	5	4	0.0047	0.36
9	SA_G1_AND_S_PHASES	Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition.	ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53	14	CDKN1B(2), PRB1(2)	911174	4	4	4	0	0	0	2	0	2	0.0053	0.36
10	SMALL_LIGAND_GPCRS		C9orf47, CNR1, CNR2, DNMT1, EDG1, EDG2, EDG5, EDG6, MTNR1A, MTNR1B, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, TBXA2R	14	DNMT1(2), MTNR1A(1), PTGER2(1), TBXA2R(1)	1476736	5	5	5	0	0	2	0	2	1	0.0063	0.36

Notes: (Please see notes under significantly mutated gene table)

Significantly mutated genes (q≤0.1)	36
Mutations seen in COSMIC	0
Significantly mutated genes on COSMIC territory	0
Genes with clustered mutations (≤3 aa apart)	1
Significantly mutated genesets	8
. . . . . . . . . (excluding sig.mutated genes)	3