MutSig results for LUAD

Number of individuals: 120

Summary of findings

Significantly mutated genes (q≤0.1) 193
Mutations seen in COSMIC 0
Significantly mutated genes on COSMIC territory 0
Genes with clustered mutations (≤3 aa apart) 1
Significantly mutated genesets 107
. . . . . . . . . (excluding sig.mutated genes) 33

Mutation preprocessing

Read 122 MAFs of type "Broad"
Total number of mutations in input MAFs:	36215
After removing 3656 noncoding mutations:	32559
After collapsing adjacent/redundant mutations:	32554

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

Mutation filtering

Number of mutations before filtering:		32554
After removing 56 mutations outside gene set:	32498
After removing 9237 mutations outside category set:	23261
After removing 16119 "impossible" mutations in
gene-patient-category bins of zero coverage:	7142

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

Final mutation list

Final set of mutations used in analysis

Mutation breakdown by type

type count
De_novo_Start_InFrame 3
De_novo_Start_OutOfFrame 14
Missense_Mutation 4957
Nonsense_Mutation 362
Read-through 6
Splice_Site_DNP 8
Splice_Site_SNP 170
Start_Codon_DNP 1
Synonymous 1621
Total 7142

type	count
De_novo_Start_InFrame	3
De_novo_Start_OutOfFrame	14
Missense_Mutation	4957
Nonsense_Mutation	362
Read-through	6
Splice_Site_DNP	8
Splice_Site_SNP	170
Start_Codon_DNP	1
Synonymous	1621
Total	7142

Nonsilent mutations: categories and mutation rates

category n N rate rate_per_mb relative_rate
A->T 1368 43,342,806 0.000032 31.6 0.54
C->(A/T) 2075 50,410,660 0.000041 41.2 0.70
A->(C/G) 1119 43,342,806 0.000026 25.8 0.44
C->G 396 50,410,660 7.86e-06 7.86 0.13
indel+null 563 93,753,466 6.01e-06 6.01 0.10
Total 5521 93,753,466 0.000059 58.9 1.00

category	n	N	rate	rate_per_mb	relative_rate
A->T	1368	43,342,806	0.000032	31.6	0.54
C->(A/T)	2075	50,410,660	0.000041	41.2	0.70
A->(C/G)	1119	43,342,806	0.000026	25.8	0.44
C->G	396	50,410,660	7.86e-06	7.86	0.13
indel+null	563	93,753,466	6.01e-06	6.01	0.10
Total	5521	93,753,466	0.000059	58.9	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 p q
1 USH2A Usher syndrome 2A (autosomal recessive, mild) 120 13 13 13 3 7 0 5 0 1 <1.00e-11 <9.93e-09
2 ADAMTS12 ADAM metallopeptidase with thrombospondin type 1 motif, 12 1200 17 16 17 3 4 10 1 0 2 <1.00e-11 <9.93e-09
3 SLIT3 slit homolog 3 (Drosophila) 480 6 6 6 10 2 2 0 1 1 <1.00e-11 <9.93e-09
4 FRAS1 Fraser syndrome 1 1200 12 10 12 1 6 1 3 1 1 <1.00e-11 <9.93e-09
5 LRP1B low density lipoprotein-related protein 1B (deleted in tumors) 14760 45 31 45 8 14 16 10 0 5 <1.00e-11 <9.93e-09
6 PTPRD protein tyrosine phosphatase, receptor type, D 6960 17 14 17 4 4 8 1 1 3 <1.00e-11 <9.93e-09
7 SVEP1 sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 3720 8 8 8 2 3 1 1 0 3 <1.00e-11 <9.93e-09
8 GPR112 G protein-coupled receptor 112 8520 17 16 17 6 4 5 4 2 2 <1.00e-11 <9.93e-09
9 CSMD1 CUB and Sushi multiple domains 1 12592 24 19 24 11 5 13 3 0 3 <1.00e-11 <9.93e-09
10 NOTCH4 Notch homolog 4 (Drosophila) 5396 10 9 10 1 2 6 2 0 0 <1.00e-11 <9.93e-09
11 ABCB5 ATP-binding cassette, sub-family B (MDR/TAP), member 5 6722 11 11 11 3 3 3 3 0 2 <1.00e-11 <9.93e-09
12 CSMD3 CUB and Sushi multiple domains 3 25745 39 25 38 11 16 9 9 1 4 <1.00e-11 <9.93e-09
13 LAMA2 laminin, alpha 2 (merosin, congenital muscular dystrophy) 10440 15 14 15 6 8 3 3 0 1 <1.00e-11 <9.93e-09
14 PAPPA2 pappalysin 2 10680 12 10 12 3 4 5 3 0 0 <1.00e-11 <9.93e-09
15 RYR3 ryanodine receptor 3 14280 15 14 15 6 4 6 4 0 1 <1.00e-11 <9.93e-09
16 KEAP1 kelch-like ECH-associated protein 1 18652 18 18 17 0 1 13 1 1 2 <1.00e-11 <9.93e-09
17 RYR2 ryanodine receptor 2 (cardiac) 67454 44 36 44 11 10 16 12 2 4 <1.00e-11 <9.93e-09
18 MUC16 mucin 16, cell surface associated 153487 54 42 53 12 10 25 10 4 5 <1.00e-11 <9.93e-09
19 TTN titin 299417 83 42 83 23 27 23 21 7 5 <1.00e-11 <9.93e-09
20 PCDH15 protocadherin 15 23760 15 13 15 7 6 3 1 2 3 1.19e-11 1.12e-08
21 CACNA1E calcium channel, voltage-dependent, R type, alpha 1E subunit 40579 19 16 19 4 5 5 6 1 2 3.31e-11 2.97e-08
22 FLT4 fms-related tyrosine kinase 4 454 5 5 5 0 1 1 2 1 0 5.48e-11 4.70e-08
23 SPTBN4 spectrin, beta, non-erythrocytic 4 129 4 4 4 1 3 0 0 0 1 7.03e-11 5.77e-08
24 VWF von Willebrand factor 1469 6 6 6 2 0 3 1 2 0 8.09e-11 6.36e-08
25 DMD dystrophin (muscular dystrophy, Duchenne and Becker types) 20160 12 9 12 4 3 6 0 2 1 7.16e-10 5.40e-07
26 SDK1 sidekick homolog 1, cell adhesion molecule (chicken) 1753 6 5 6 4 0 5 1 0 0 8.93e-10 6.48e-07
27 STXBP5L syntaxin binding protein 5-like 5040 8 8 8 1 3 2 2 1 0 1.78e-09 1.24e-06
28 PTPRB protein tyrosine phosphatase, receptor type, B 5604 8 8 8 2 2 3 2 0 1 6.09e-09 4.08e-06
29 BIRC6 baculoviral IAP repeat-containing 6 (apollon) 15663 11 10 11 0 4 6 1 0 0 6.28e-09 4.08e-06
30 MYH13 myosin, heavy chain 13, skeletal muscle 5400 7 7 7 5 4 0 2 1 0 6.49e-09 4.08e-06

(click for full table with 18865 genes)

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	USH2A	Usher syndrome 2A (autosomal recessive, mild)	120	13	13	13	3	7	0	5	0	1	<1.00e-11	<9.93e-09
2	ADAMTS12	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1200	17	16	17	3	4	10	1	0	2	<1.00e-11	<9.93e-09
3	SLIT3	slit homolog 3 (Drosophila)	480	6	6	6	10	2	2	0	1	1	<1.00e-11	<9.93e-09
4	FRAS1	Fraser syndrome 1	1200	12	10	12	1	6	1	3	1	1	<1.00e-11	<9.93e-09
5	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	14760	45	31	45	8	14	16	10	0	5	<1.00e-11	<9.93e-09
6	PTPRD	protein tyrosine phosphatase, receptor type, D	6960	17	14	17	4	4	8	1	1	3	<1.00e-11	<9.93e-09
7	SVEP1	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3720	8	8	8	2	3	1	1	0	3	<1.00e-11	<9.93e-09
8	GPR112	G protein-coupled receptor 112	8520	17	16	17	6	4	5	4	2	2	<1.00e-11	<9.93e-09
9	CSMD1	CUB and Sushi multiple domains 1	12592	24	19	24	11	5	13	3	0	3	<1.00e-11	<9.93e-09
10	NOTCH4	Notch homolog 4 (Drosophila)	5396	10	9	10	1	2	6	2	0	0	<1.00e-11	<9.93e-09
11	ABCB5	ATP-binding cassette, sub-family B (MDR/TAP), member 5	6722	11	11	11	3	3	3	3	0	2	<1.00e-11	<9.93e-09
12	CSMD3	CUB and Sushi multiple domains 3	25745	39	25	38	11	16	9	9	1	4	<1.00e-11	<9.93e-09
13	LAMA2	laminin, alpha 2 (merosin, congenital muscular dystrophy)	10440	15	14	15	6	8	3	3	0	1	<1.00e-11	<9.93e-09
14	PAPPA2	pappalysin 2	10680	12	10	12	3	4	5	3	0	0	<1.00e-11	<9.93e-09
15	RYR3	ryanodine receptor 3	14280	15	14	15	6	4	6	4	0	1	<1.00e-11	<9.93e-09
16	KEAP1	kelch-like ECH-associated protein 1	18652	18	18	17	0	1	13	1	1	2	<1.00e-11	<9.93e-09
17	RYR2	ryanodine receptor 2 (cardiac)	67454	44	36	44	11	10	16	12	2	4	<1.00e-11	<9.93e-09
18	MUC16	mucin 16, cell surface associated	153487	54	42	53	12	10	25	10	4	5	<1.00e-11	<9.93e-09
19	TTN	titin	299417	83	42	83	23	27	23	21	7	5	<1.00e-11	<9.93e-09
20	PCDH15	protocadherin 15	23760	15	13	15	7	6	3	1	2	3	1.19e-11	1.12e-08
21	CACNA1E	calcium channel, voltage-dependent, R type, alpha 1E subunit	40579	19	16	19	4	5	5	6	1	2	3.31e-11	2.97e-08
22	FLT4	fms-related tyrosine kinase 4	454	5	5	5	0	1	1	2	1	0	5.48e-11	4.70e-08
23	SPTBN4	spectrin, beta, non-erythrocytic 4	129	4	4	4	1	3	0	0	0	1	7.03e-11	5.77e-08
24	VWF	von Willebrand factor	1469	6	6	6	2	0	3	1	2	0	8.09e-11	6.36e-08
25	DMD	dystrophin (muscular dystrophy, Duchenne and Becker types)	20160	12	9	12	4	3	6	0	2	1	7.16e-10	5.40e-07
26	SDK1	sidekick homolog 1, cell adhesion molecule (chicken)	1753	6	5	6	4	0	5	1	0	0	8.93e-10	6.48e-07
27	STXBP5L	syntaxin binding protein 5-like	5040	8	8	8	1	3	2	2	1	0	1.78e-09	1.24e-06
28	PTPRB	protein tyrosine phosphatase, receptor type, B	5604	8	8	8	2	2	3	2	0	1	6.09e-09	4.08e-06
29	BIRC6	baculoviral IAP repeat-containing 6 (apollon)	15663	11	10	11	0	4	6	1	0	0	6.28e-09	4.08e-06
30	MYH13	myosin, heavy chain 13, skeletal muscle	5400	7	7	7	5	4	0	2	1	0	6.49e-09	4.08e-06

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"
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 = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

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 4550 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 4550 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

gene patient chr start end type n_cos

(click for full table with 0 mutations)

Genes with clustered mutations

rank gene desc n mindist npairs3 npairs12
1 MUC2 mucin 2, oligomeric mucus/gel-forming 5 2 1 1
2 GRIN2B glutamate receptor, ionotropic, N-methyl D-aspartate 2B 8 9 0 1
3 PKHD1L1 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 19 116 0 0
4 MXRA5 matrix-remodelling associated 5 9 716 0 0
5 SH3TC2 SH3 domain and tetratricopeptide repeats 2 5 913 0 0
6 MDN1 MDN1, midasin homolog (yeast) 4 927 0 0
7 PDCD11 programmed cell death 11 4 1401 0 0
8 GPR98 G protein-coupled receptor 98 9 1445 0 0
9 A2ML1 alpha-2-macroglobulin-like 1 3 Inf 0 0
10 AAK1 AP2 associated kinase 1 4 Inf 0 0
11 AARS2 alanyl-tRNA synthetase 2, mitochondrial (putative) 2 Inf 0 0
12 ABCA10 ATP-binding cassette, sub-family A (ABC1), member 10 4 Inf 0 0
13 ABCA13 ATP-binding cassette, sub-family A (ABC1), member 13 14 Inf 0 0
14 ABCA3 ATP-binding cassette, sub-family A (ABC1), member 3 4 Inf 0 0
15 ABCA4 ATP-binding cassette, sub-family A (ABC1), member 4 3 Inf 0 0
16 ABCA6 ATP-binding cassette, sub-family A (ABC1), member 6 3 Inf 0 0
17 ABCA7 ATP-binding cassette, sub-family A (ABC1), member 7 2 Inf 0 0
18 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 3 Inf 0 0
19 ABCB5 ATP-binding cassette, sub-family B (MDR/TAP), member 5 11 Inf 0 0
20 ABCC12 ATP-binding cassette, sub-family C (CFTR/MRP), member 12 5 Inf 0 0
21 ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member 3 3 Inf 0 0
22 ABCC5 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 2 Inf 0 0
23 ABCC8 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 5 Inf 0 0
24 ABCC9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 5 Inf 0 0
25 ABCG4 ATP-binding cassette, sub-family G (WHITE), member 4 2 Inf 0 0
26 ABCG5 ATP-binding cassette, sub-family G (WHITE), member 5 (sterolin 1) 2 Inf 0 0
27 ABLIM3 actin binding LIM protein family, member 3 3 Inf 0 0
28 ACACA acetyl-Coenzyme A carboxylase alpha 2 Inf 0 0
29 ACACB acetyl-Coenzyme A carboxylase beta 4 Inf 0 0
30 ACCN2 amiloride-sensitive cation channel 2, neuronal 2 Inf 0 0

(click for full table with 2257 genes)

rank	gene	desc	n	mindist	npairs3	npairs12
1	MUC2	mucin 2, oligomeric mucus/gel-forming	5	2	1	1
2	GRIN2B	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	8	9	0	1
3	PKHD1L1	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	19	116	0	0
4	MXRA5	matrix-remodelling associated 5	9	716	0	0
5	SH3TC2	SH3 domain and tetratricopeptide repeats 2	5	913	0	0
6	MDN1	MDN1, midasin homolog (yeast)	4	927	0	0
7	PDCD11	programmed cell death 11	4	1401	0	0
8	GPR98	G protein-coupled receptor 98	9	1445	0	0
9	A2ML1	alpha-2-macroglobulin-like 1	3	Inf	0	0
10	AAK1	AP2 associated kinase 1	4	Inf	0	0
11	AARS2	alanyl-tRNA synthetase 2, mitochondrial (putative)	2	Inf	0	0
12	ABCA10	ATP-binding cassette, sub-family A (ABC1), member 10	4	Inf	0	0
13	ABCA13	ATP-binding cassette, sub-family A (ABC1), member 13	14	Inf	0	0
14	ABCA3	ATP-binding cassette, sub-family A (ABC1), member 3	4	Inf	0	0
15	ABCA4	ATP-binding cassette, sub-family A (ABC1), member 4	3	Inf	0	0
16	ABCA6	ATP-binding cassette, sub-family A (ABC1), member 6	3	Inf	0	0
17	ABCA7	ATP-binding cassette, sub-family A (ABC1), member 7	2	Inf	0	0
18	ABCB1	ATP-binding cassette, sub-family B (MDR/TAP), member 1	3	Inf	0	0
19	ABCB5	ATP-binding cassette, sub-family B (MDR/TAP), member 5	11	Inf	0	0
20	ABCC12	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	5	Inf	0	0
21	ABCC3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	3	Inf	0	0
22	ABCC5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	2	Inf	0	0
23	ABCC8	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	5	Inf	0	0
24	ABCC9	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	5	Inf	0	0
25	ABCG4	ATP-binding cassette, sub-family G (WHITE), member 4	2	Inf	0	0
26	ABCG5	ATP-binding cassette, sub-family G (WHITE), member 5 (sterolin 1)	2	Inf	0	0
27	ABLIM3	actin binding LIM protein family, member 3	3	Inf	0	0
28	ACACA	acetyl-Coenzyme A carboxylase alpha	2	Inf	0	0
29	ACACB	acetyl-Coenzyme A carboxylase beta	4	Inf	0	0
30	ACCN2	amiloride-sensitive cation channel 2, neuronal	2	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 N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 p q
1 ARENRF2PATHWAY Nrf1 and nrf2 are transcription factors that bind to antioxidant response elements (AREs), promoters of genes involved in oxidative damage control. 13 CREB1(1), KEAP1(18), PRKCA(2) 43641 21 20 20 1 3 13 1 2 2 <1.00e-11 <6.21e-10
2 NO1PATHWAY Shear stress in endothelial cells increases cytoplasmic calcium, which activates nitric oxide synthase III to release NO, which in turn regulates cardiac contractions. 28 CHRNA1(3), FLT4(5), NOS3(1), RYR2(44), SLC7A1(1) 239584 54 38 54 11 13 17 14 5 5 <1.00e-11 <6.21e-10
3 HSA04720_LONG_TERM_ POTENTIATION Genes involved in long-term potentiation 67 ADCY8(7), ARAF(1), BRAF(4), CACNA1C(8), CAMK2A(1), CAMK2B(3), CAMK2D(1), CAMK4(3), CREBBP(2), GRIA1(3), GRIN2B(8), GRM1(8), ITPR1(2), ITPR2(6), ITPR3(4), KRAS(5), PLCB1(5), PLCB4(3), PPP3CC(1), PRKCA(2), RPS6KA2(1) 401402 78 50 75 25 25 24 15 3 11 <1.00e-11 <6.21e-10
4 STRIATED_MUSCLE_ CONTRACTION 37 ACTN3(2), DMD(12), MYBPC2(1), MYBPC3(3), MYH6(7), MYH7(5), MYH8(10), MYOM1(2), NEB(10), TPM2(1), TPM4(1), TTN(83) 734050 137 66 137 42 37 49 28 11 12 <1.00e-11 <6.21e-10
5 HSA04020_CALCIUM_ SIGNALING_PATHWAY Genes involved in calcium signaling pathway 169 ADCY2(4), ADCY3(1), ADCY4(1), ADCY8(7), ATP2A3(1), ATP2B1(1), ATP2B2(4), ATP2B4(1), CACNA1A(1), CACNA1C(8), CACNA1D(6), CACNA1E(19), CACNA1F(2), CACNA1G(4), CACNA1H(1), CACNA1I(1), CAMK2A(1), CAMK2B(3), CAMK2D(1), CAMK4(3), EGFR(7), GNA11(1), GNAS(3), GRM1(8), ITPR1(2), ITPR2(6), ITPR3(4), MYLK(4), NOS3(1), PDE1A(1), PDE1B(1), PDGFRB(3), PLCB1(5), PLCB4(3), PLCD1(1), PLCD4(2), PLCE1(2), PPP3CC(1), PRKCA(2), PTK2B(2), RYR1(17), RYR2(44), RYR3(15), SLC8A2(1), SLC8A3(4) 1446030 210 81 208 66 52 72 52 10 24 <1.00e-11 <6.21e-10
6 HSA04912_GNRH_SIGNALING_ PATHWAY Genes involved in GnRH signaling pathway 95 ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), CACNA1C(8), CACNA1D(6), CACNA1F(2), CAMK2A(1), CAMK2B(3), CAMK2D(1), EGFR(7), GNA11(1), GNAS(3), ITPR1(2), ITPR2(6), ITPR3(4), KRAS(5), MAP2K4(1), MAP2K6(1), PLA2G4A(3), PLCB1(5), PLCB4(3), PRKCA(2), PTK2B(2), SOS1(3) 606893 86 53 81 34 20 23 22 6 15 <1.00e-11 <6.21e-10
7 CALCIUM_REGULATION_ IN_CARDIAC_CELLS 139 ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), ATP2A3(1), ATP2B1(1), ATP2B2(4), CACNA1A(1), CACNA1C(8), CACNA1D(6), CACNA1E(19), CAMK2A(1), CAMK2B(3), CAMK2D(1), CAMK4(3), GJB1(1), GNA11(1), GRK4(2), GRK6(1), ITPR1(2), ITPR2(6), ITPR3(4), PRKCA(2), PRKCE(1), RYR1(17), RYR2(44), RYR3(15), SLC8A3(4) 1280902 165 70 165 58 38 58 41 7 21 <1.00e-11 <6.21e-10
8 HSA04512_ECM_RECEPTOR_ INTERACTION Genes involved in ECM-receptor interaction 87 AGRN(1), CD36(1), COL11A2(2), COL4A1(2), COL4A4(5), COL4A6(8), COL5A3(5), FNDC3A(2), GP1BA(1), GP5(1), HSPG2(5), ITGA1(1), ITGA11(2), ITGA2(3), ITGA5(1), ITGA7(1), ITGA8(6), ITGB4(1), LAMA1(11), LAMA2(15), LAMA3(5), LAMA5(3), LAMB1(4), LAMB2(8), LAMB3(3), LAMB4(8), LAMC3(3), RELN(16), TNC(12), TNXB(5), VWF(6) 1203307 147 58 147 43 32 72 17 12 14 <1.00e-11 <6.21e-10
9 SMOOTH_MUSCLE_CONTRACTION 138 ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), ATP2A3(1), CAMK2A(1), CAMK2B(3), CAMK2D(1), CNN1(1), GRK4(2), GRK6(1), ITPR1(2), ITPR2(6), ITPR3(4), NOS3(1), PLCD1(1), PRKCA(2), PRKCE(1), RYR1(17), RYR2(44), RYR3(15), TNXB(5) 1026257 125 62 125 46 28 45 26 9 17 <1.00e-11 <6.21e-10
10 HSA04540_GAP_JUNCTION Genes involved in gap junction 92 ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), EGFR(7), GNA11(1), GNAS(3), GRM1(8), GUCY2C(3), ITPR1(2), ITPR2(6), ITPR3(4), KRAS(5), PDGFRB(3), PLCB1(5), PLCB4(3), PRKCA(2), SOS1(3), TUBA4A(1), TUBB4(1) 536396 74 49 69 28 19 16 18 7 14 1.11e-11 6.21e-10

(click for full table with 616 genesets)

rank	geneset	description	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	ARENRF2PATHWAY	Nrf1 and nrf2 are transcription factors that bind to antioxidant response elements (AREs), promoters of genes involved in oxidative damage control.	13	CREB1(1), KEAP1(18), PRKCA(2)	43641	21	20	20	1	3	13	1	2	2	<1.00e-11	<6.21e-10
2	NO1PATHWAY	Shear stress in endothelial cells increases cytoplasmic calcium, which activates nitric oxide synthase III to release NO, which in turn regulates cardiac contractions.	28	CHRNA1(3), FLT4(5), NOS3(1), RYR2(44), SLC7A1(1)	239584	54	38	54	11	13	17	14	5	5	<1.00e-11	<6.21e-10
3	HSA04720_LONG_TERM_ POTENTIATION	Genes involved in long-term potentiation	67	ADCY8(7), ARAF(1), BRAF(4), CACNA1C(8), CAMK2A(1), CAMK2B(3), CAMK2D(1), CAMK4(3), CREBBP(2), GRIA1(3), GRIN2B(8), GRM1(8), ITPR1(2), ITPR2(6), ITPR3(4), KRAS(5), PLCB1(5), PLCB4(3), PPP3CC(1), PRKCA(2), RPS6KA2(1)	401402	78	50	75	25	25	24	15	3	11	<1.00e-11	<6.21e-10
4	STRIATED_MUSCLE_ CONTRACTION		37	ACTN3(2), DMD(12), MYBPC2(1), MYBPC3(3), MYH6(7), MYH7(5), MYH8(10), MYOM1(2), NEB(10), TPM2(1), TPM4(1), TTN(83)	734050	137	66	137	42	37	49	28	11	12	<1.00e-11	<6.21e-10
5	HSA04020_CALCIUM_ SIGNALING_PATHWAY	Genes involved in calcium signaling pathway	169	ADCY2(4), ADCY3(1), ADCY4(1), ADCY8(7), ATP2A3(1), ATP2B1(1), ATP2B2(4), ATP2B4(1), CACNA1A(1), CACNA1C(8), CACNA1D(6), CACNA1E(19), CACNA1F(2), CACNA1G(4), CACNA1H(1), CACNA1I(1), CAMK2A(1), CAMK2B(3), CAMK2D(1), CAMK4(3), EGFR(7), GNA11(1), GNAS(3), GRM1(8), ITPR1(2), ITPR2(6), ITPR3(4), MYLK(4), NOS3(1), PDE1A(1), PDE1B(1), PDGFRB(3), PLCB1(5), PLCB4(3), PLCD1(1), PLCD4(2), PLCE1(2), PPP3CC(1), PRKCA(2), PTK2B(2), RYR1(17), RYR2(44), RYR3(15), SLC8A2(1), SLC8A3(4)	1446030	210	81	208	66	52	72	52	10	24	<1.00e-11	<6.21e-10
6	HSA04912_GNRH_SIGNALING_ PATHWAY	Genes involved in GnRH signaling pathway	95	ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), CACNA1C(8), CACNA1D(6), CACNA1F(2), CAMK2A(1), CAMK2B(3), CAMK2D(1), EGFR(7), GNA11(1), GNAS(3), ITPR1(2), ITPR2(6), ITPR3(4), KRAS(5), MAP2K4(1), MAP2K6(1), PLA2G4A(3), PLCB1(5), PLCB4(3), PRKCA(2), PTK2B(2), SOS1(3)	606893	86	53	81	34	20	23	22	6	15	<1.00e-11	<6.21e-10
7	CALCIUM_REGULATION_ IN_CARDIAC_CELLS		139	ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), ATP2A3(1), ATP2B1(1), ATP2B2(4), CACNA1A(1), CACNA1C(8), CACNA1D(6), CACNA1E(19), CAMK2A(1), CAMK2B(3), CAMK2D(1), CAMK4(3), GJB1(1), GNA11(1), GRK4(2), GRK6(1), ITPR1(2), ITPR2(6), ITPR3(4), PRKCA(2), PRKCE(1), RYR1(17), RYR2(44), RYR3(15), SLC8A3(4)	1280902	165	70	165	58	38	58	41	7	21	<1.00e-11	<6.21e-10
8	HSA04512_ECM_RECEPTOR_ INTERACTION	Genes involved in ECM-receptor interaction	87	AGRN(1), CD36(1), COL11A2(2), COL4A1(2), COL4A4(5), COL4A6(8), COL5A3(5), FNDC3A(2), GP1BA(1), GP5(1), HSPG2(5), ITGA1(1), ITGA11(2), ITGA2(3), ITGA5(1), ITGA7(1), ITGA8(6), ITGB4(1), LAMA1(11), LAMA2(15), LAMA3(5), LAMA5(3), LAMB1(4), LAMB2(8), LAMB3(3), LAMB4(8), LAMC3(3), RELN(16), TNC(12), TNXB(5), VWF(6)	1203307	147	58	147	43	32	72	17	12	14	<1.00e-11	<6.21e-10
9	SMOOTH_MUSCLE_CONTRACTION		138	ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), ATP2A3(1), CAMK2A(1), CAMK2B(3), CAMK2D(1), CNN1(1), GRK4(2), GRK6(1), ITPR1(2), ITPR2(6), ITPR3(4), NOS3(1), PLCD1(1), PRKCA(2), PRKCE(1), RYR1(17), RYR2(44), RYR3(15), TNXB(5)	1026257	125	62	125	46	28	45	26	9	17	<1.00e-11	<6.21e-10
10	HSA04540_GAP_JUNCTION	Genes involved in gap junction	92	ADCY2(4), ADCY3(1), ADCY4(1), ADCY5(4), ADCY8(7), EGFR(7), GNA11(1), GNAS(3), GRM1(8), GUCY2C(3), ITPR1(2), ITPR2(6), ITPR3(4), KRAS(5), PDGFRB(3), PLCB1(5), PLCB4(3), PRKCA(2), SOS1(3), TUBA4A(1), TUBB4(1)	536396	74	49	69	28	19	16	18	7	14	1.11e-11	6.21e-10

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

Significantly mutated genesets (excluding significantly mutated genes)

rank geneset description N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 p q
1 HSA02010_ABC_TRANSPORTERS_ GENERAL Genes involved in ABC transporters - general 42 ABCA13(14), ABCA3(4), ABCA4(3), ABCA6(3), ABCA7(2), ABCB1(3), ABCC1(1), ABCC10(1), ABCC12(5), ABCC2(1), ABCC3(3), ABCC5(2), ABCC8(5), ABCC9(5), ABCG4(2), ABCG5(2), ABCG8(1), TAP2(1) 519552 58 41 58 12 18 18 11 4 7 0.000080 0.046
2 MONOCYTEPATHWAY Monocytes are a class of immune phagocytes that can develop into macrophages and express LFA-1, CD44, and other surface signaling proteins. 10 ITGAL(6), ITGAM(3), SELE(3) 64350 12 9 12 3 5 2 1 2 2 0.00022 0.046
3 NEUTROPHILPATHWAY Neutrophils are phagocytotic leukocytes that destroy foreign cells with reactive oxygen species or enzymatic digestion and express CD11 and CD18. 8 ITGAL(6), ITGAM(3), SELE(3) 64350 12 9 12 3 5 2 1 2 2 0.00022 0.046
4 LAIRPATHWAY The local acute inflammatory response is mediated by activated macrophages and mast cells or by complement activation. 15 C3(2), C6(2), C7(3), ITGAL(6) 64791 13 12 13 3 4 5 1 2 1 0.00035 0.048
5 HSA04670_LEUKOCYTE_ TRANSENDOTHELIAL_ MIGRATION Genes involved in Leukocyte transendothelial migration 110 ACTN3(2), CDH5(1), CTNND1(3), CYBB(1), GRLF1(3), ITGAL(6), ITGAM(3), MYL7(1), PIK3R5(2), PRKCA(2), PTK2(2), PTK2B(2), RHOH(2) 290756 30 23 30 10 12 10 2 5 1 0.00039 0.048
6 HSA00680_METHANE_ METABOLISM Genes involved in methane metabolism 10 TPO(6) 22127 6 6 6 2 0 4 0 2 0 0.0011 0.074
7 HSA00940_PHENYLPROPANOID_ BIOSYNTHESIS Genes involved in phenylpropanoid biosynthesis 7 TPO(6) 22127 6 6 6 2 0 4 0 2 0 0.0011 0.074
8 BLYMPHOCYTEPATHWAY B cells express the major histocompatibility complex (class II MHC), immunoglobulins, adhesion proteins, and other factors on their cell surface. 10 CR1(3), ITGAL(6), PTPRC(6) 90809 15 14 15 1 6 4 2 1 2 0.0011 0.074
9 GPCRDB_CLASS_C_METABOTROPIC_ GLUTAMATE_PHEROMONE 12 CASR(4), GRM2(2) 17756 6 6 6 0 3 2 1 0 0 0.0012 0.074
10 AGPCRPATHWAY G-protein coupled receptors (GPCRs) transduce extracellular signals across the plasma membrane; attenuation occurs by signal molecule degradation or receptor-mediated endocytosis. 11 GNAS(3), PRKCA(2) 17733 5 5 5 3 3 0 2 0 0 0.0013 0.074

(click for full table with 616 genesets)

rank	geneset	description	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	HSA02010_ABC_TRANSPORTERS_ GENERAL	Genes involved in ABC transporters - general	42	ABCA13(14), ABCA3(4), ABCA4(3), ABCA6(3), ABCA7(2), ABCB1(3), ABCC1(1), ABCC10(1), ABCC12(5), ABCC2(1), ABCC3(3), ABCC5(2), ABCC8(5), ABCC9(5), ABCG4(2), ABCG5(2), ABCG8(1), TAP2(1)	519552	58	41	58	12	18	18	11	4	7	0.000080	0.046
2	MONOCYTEPATHWAY	Monocytes are a class of immune phagocytes that can develop into macrophages and express LFA-1, CD44, and other surface signaling proteins.	10	ITGAL(6), ITGAM(3), SELE(3)	64350	12	9	12	3	5	2	1	2	2	0.00022	0.046
3	NEUTROPHILPATHWAY	Neutrophils are phagocytotic leukocytes that destroy foreign cells with reactive oxygen species or enzymatic digestion and express CD11 and CD18.	8	ITGAL(6), ITGAM(3), SELE(3)	64350	12	9	12	3	5	2	1	2	2	0.00022	0.046
4	LAIRPATHWAY	The local acute inflammatory response is mediated by activated macrophages and mast cells or by complement activation.	15	C3(2), C6(2), C7(3), ITGAL(6)	64791	13	12	13	3	4	5	1	2	1	0.00035	0.048
5	HSA04670_LEUKOCYTE_ TRANSENDOTHELIAL_ MIGRATION	Genes involved in Leukocyte transendothelial migration	110	ACTN3(2), CDH5(1), CTNND1(3), CYBB(1), GRLF1(3), ITGAL(6), ITGAM(3), MYL7(1), PIK3R5(2), PRKCA(2), PTK2(2), PTK2B(2), RHOH(2)	290756	30	23	30	10	12	10	2	5	1	0.00039	0.048
6	HSA00680_METHANE_ METABOLISM	Genes involved in methane metabolism	10	TPO(6)	22127	6	6	6	2	0	4	0	2	0	0.0011	0.074
7	HSA00940_PHENYLPROPANOID_ BIOSYNTHESIS	Genes involved in phenylpropanoid biosynthesis	7	TPO(6)	22127	6	6	6	2	0	4	0	2	0	0.0011	0.074
8	BLYMPHOCYTEPATHWAY	B cells express the major histocompatibility complex (class II MHC), immunoglobulins, adhesion proteins, and other factors on their cell surface.	10	CR1(3), ITGAL(6), PTPRC(6)	90809	15	14	15	1	6	4	2	1	2	0.0011	0.074
9	GPCRDB_CLASS_C_METABOTROPIC_ GLUTAMATE_PHEROMONE		12	CASR(4), GRM2(2)	17756	6	6	6	0	3	2	1	0	0	0.0012	0.074
10	AGPCRPATHWAY	G-protein coupled receptors (GPCRs) transduce extracellular signals across the plasma membrane; attenuation occurs by signal molecule degradation or receptor-mediated endocytosis.	11	GNAS(3), PRKCA(2)	17733	5	5	5	3	3	0	2	0	0	0.0013	0.074

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

Significantly mutated genes (q≤0.1)	193
Mutations seen in COSMIC	0
Significantly mutated genes on COSMIC territory	0
Genes with clustered mutations (≤3 aa apart)	1
Significantly mutated genesets	107
. . . . . . . . . (excluding sig.mutated genes)	33