Uterine Corpus Endometrioid Carcinoma: Mutation Analysis (MutSig v2.0)

Maintained by Dan DiCara (Broad Institute)

- Overview

+ Introduction

- Summary

MAF used for this analysis:UCEC.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 82
Mutations seen in COSMIC: 1008
Significantly mutated genes in COSMIC territory: 47
Genes with clustered mutations (≤ 3 aa apart): 4501
Significantly mutated genesets: 69
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

Read 248 MAFs of type "WashU"
Total number of mutations in input MAFs: 184824
After removing 118 mutations outside chr1-24: 184706
After removing 1940 noncoding mutations: 182766
After collapsing adjacent/redundant mutations: 182636

Mutation Filtering

Number of mutations before filtering: 182636
After removing 8680 mutations outside gene set: 173956
After removing 1038 mutations outside category set: 172918

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	1070
Frame_Shift_Ins	474
In_Frame_Del	765
In_Frame_Ins	148
Missense_Mutation	115613
Nonsense_Mutation	11935
Nonstop_Mutation	138
Silent	40121
Splice_Site	2654
Total	172918

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
*CpG->T	38721	409266464	0.000095	95	5.4	2.1
*Cp(A/C/T)->mut	51454	3453658664	0.000015	15	0.85	3.3
A->mut	24344	3744388816	6.5e-06	6.5	0.37	3.9
*CpG->(G/A)	1084	409266464	2.6e-06	2.6	0.15	2.7
indel+null	16310	7607313944	2.1e-06	2.1	0.12	NaN
double_null	884	7607313944	1.2e-07	0.12	0.0067	NaN
Total	132797	7607313944	0.000017	17	1	3.5

+ Target Coverage for Each Individual

+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

+ CoMut Plot

+ Significantly Mutated Genes

Column Descriptions:

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 non-silent mutation
nsil = number of silent mutations in this gene across the individual set
n1 = number of nonsilent mutations of type: *CpG->T
n2 = number of nonsilent mutations of type: *Cp(A/C/T)->mut
n3 = number of nonsilent mutations of type: A->mut
n4 = number of nonsilent mutations of type: *CpG->(G/A)
n5 = number of nonsilent mutations of type: indel+null
n6 = number of nonsilent mutations of type: double_null
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)

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 82. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_classic	p_ns_s	p_ks	p_cons	p_joint	p	q
1	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	309504	227	161	134	5	19	29	21	33	98	27	1.11e-15	4.9e-12	2e-07	0.71	0.000023	0.000	0.000
2	FBXW7	F-box and WD repeat domain containing 7	640832	46	39	30	1	22	12	2	1	8	1	3.77e-15	0.00048	0.00054	0.0046	0.00011	0.000	0.000
3	SPOP	speckle-type POZ protein	287928	23	21	18	0	5	8	6	0	4	0	5.66e-15	0.0041	0.0029	0.022	0.00068	1.11e-16	6.77e-13
4	CTCF	CCCTC-binding factor (zinc finger protein)	551552	49	45	39	1	8	4	7	0	28	2	1.89e-15	0.00095	0.0061	0.052	0.0059	4.44e-16	1.31e-12
5	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	815176	172	132	76	3	31	61	68	3	9	0	<1.00e-15	2.1e-11	2e-07	2e-07	0	<1.00e-15	<1.31e-12
6	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	585280	100	83	77	2	4	4	13	1	63	15	6.00e-15	0.0021	2e-07	0.38	0	<1.00e-15	<1.31e-12
7	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	595696	80	74	25	7	5	61	14	0	0	0	<1.00e-15	0.0034	2e-07	2e-07	0	<1.00e-15	<1.31e-12
8	TP53	tumor protein p53	317688	74	69	50	2	23	18	15	1	17	0	1.55e-15	2.8e-06	2e-07	2e-07	0	<1.00e-15	<1.31e-12
9	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	175336	53	53	12	1	2	46	4	1	0	0	3.44e-15	0.0012	2e-07	0.00023	0	<1.00e-15	<1.31e-12
10	PPP2R1A	protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform	453840	30	27	18	3	10	17	1	0	2	0	6.38e-14	0.0023	2e-07	0.098	0	<1.00e-15	<1.31e-12
11	PRKAR1B	protein kinase, cAMP-dependent, regulatory, type I, beta	286192	4	4	4	3	2	0	0	1	1	0	0.993	0.82	0.0055	6.6e-06	0	<1.00e-15	<1.31e-12
12	HMGN1	high-mobility group nucleosome binding domain 1	76384	2	2	2	0	0	0	0	0	2	0	0.178	0.67	0.1	0.0047	0	<1.00e-15	<1.31e-12
13	IL10	interleukin 10	138136	3	2	3	3	1	1	0	0	1	0	0.709	0.98	0.14	0.0046	0	<1.00e-15	<1.31e-12
14	NMD3	NMD3 homolog (S. cerevisiae)	389856	2	2	2	0	1	0	0	0	1	0	0.949	0.63	0.27	0.081	0	<1.00e-15	<1.31e-12
15	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	691920	34	31	19	3	3	5	13	9	3	1	6.77e-15	0.0097	0.018	0.24	0.031	7.77e-15	9.47e-12
16	ARID1A	AT rich interactive domain 1A (SWI-like)	1428976	94	83	79	5	2	7	5	1	65	14	1.78e-15	0.00014	0.17	0.42	0.3	1.90e-14	2.17e-11
17	CHD4	chromodomain helicase DNA binding protein 4	1460720	43	35	38	2	16	16	8	0	2	1	1.55e-11	0.0046	0.011	0.55	0.022	1.02e-11	1.10e-08
18	NFE2L2	nuclear factor (erythroid-derived 2)-like 2	449872	15	15	12	0	2	3	5	3	2	0	2.78e-08	0.016	0.000068	0.028	0.000025	1.98e-11	2.01e-08
19	P2RY11	purinergic receptor P2Y, G-protein coupled, 11	5704	9	9	9	3	3	4	0	1	1	0	2.23e-11	0.3	NaN	NaN	NaN	2.23e-11	2.15e-08
20	CCND1	cyclin D1	222952	15	15	13	1	1	7	3	0	4	0	7.63e-09	0.084	0.00013	0.23	0.00022	4.65e-11	4.25e-08
21	SOX17	SRY (sex determining region Y)-box 17	91512	7	7	3	0	0	6	0	0	1	0	4.35e-07	0.15	0.0048	0.013	0.00078	7.78e-09	6.78e-06
22	FOXA2	forkhead box A2	227912	12	12	12	1	1	3	2	0	6	0	3.75e-08	0.27	0.097	0.11	0.086	6.63e-08	5.51e-05
23	FAM9A	family with sequence similarity 9, member A	255688	20	14	20	1	2	12	1	0	4	1	7.46e-08	0.096	0.1	1	0.21	3.03e-07	0.000241
24	DNER	delta/notch-like EGF repeat containing	492528	21	18	20	1	4	9	5	0	3	0	0.000159	0.01	0.043	0.0001	0.00032	8.99e-07	0.000685
25	SMTNL2	smoothelin-like 2	223944	9	9	3	2	0	2	0	0	7	0	0.00174	0.37	6.6e-06	0.48	0.000058	1.72e-06	0.00125
26	RBMX	RNA binding motif protein, X-linked	313224	14	13	8	0	1	4	2	0	7	0	2.89e-05	0.3	0.0044	0.15	0.0042	2.05e-06	0.00144
27	PGR	progesterone receptor	393328	13	12	11	2	3	3	2	1	4	0	0.00771	0.33	0.00026	0.00072	0.000023	2.98e-06	0.00202
28	TNFAIP6	tumor necrosis factor, alpha-induced protein 6	212784	12	12	8	0	2	4	0	0	6	0	3.44e-06	0.18	0.21	0.97	0.3	1.54e-05	0.0101
29	SGK1	serum/glucocorticoid regulated kinase 1	480376	16	15	14	3	2	5	1	1	7	0	0.000234	0.52	0.49	0.0012	0.0048	1.65e-05	0.0104
30	PDE8B	phosphodiesterase 8B	595944	19	16	19	1	7	5	6	0	1	0	0.0265	0.018	0.0035	0.00022	0.000047	1.81e-05	0.0110
31	HPD	4-hydroxyphenylpyruvate dioxygenase	307024	7	7	3	0	0	0	1	0	6	0	0.0315	0.64	0.0069	0.00018	0.000057	2.55e-05	0.0149
32	RPL14	ribosomal protein L14	168392	8	7	4	0	0	1	0	2	5	0	0.000151	0.36	0.0064	0.94	0.012	2.60e-05	0.0149
33	TAP1	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	150784	8	8	8	0	2	3	0	0	3	0	0.00403	0.12	0.00035	0.12	0.0005	2.85e-05	0.0158
34	MAX	MYC associated factor X	209064	12	11	8	0	3	3	5	0	1	0	1.23e-05	0.048	0.26	0.065	0.17	2.97e-05	0.0160
35	ZNF286A	zinc finger protein 286A	393328	16	12	14	1	3	6	6	0	1	0	0.00104	0.12	0.0012	0.59	0.0027	3.85e-05	0.0201

+ COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4. Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 47. Number of genes displayed: 10

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	227	728	218	180544	14940	0	0
2	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	100	33	39	8184	111	2.5e-13	4e-10
3	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	34	49	24	12152	113	3.4e-13	4e-10
4	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	53	51	49	12648	556649	3.5e-13	4e-10
5	FBXW7	F-box and WD repeat domain containing 7	46	91	29	22568	852	5.3e-13	4e-10
6	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	80	101	67	25048	23813	5.6e-13	4e-10
7	TP53	tumor protein p53	74	308	72	76384	24186	7e-13	4e-10
8	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	172	184	150	45632	35669	7.2e-13	4e-10
9	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	9	28	6	6944	6490	4e-09	2e-06
10	RB1	retinoblastoma 1 (including osteosarcoma)	26	267	11	66216	30	4.3e-08	0.000019

Note:

n - number of (nonsilent) mutations in this gene across 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 times 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)

+ Clustered Mutations

num	gene	desc	n	nmuts0	nmuts3	nmuts12	npairs0	npairs3	npairs12
11548	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	226	1515	1989	2858	1515	1989	2858
7589	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	52	661	949	994	661	949	994
10791	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	172	573	1075	1553	573	1075	1553
3515	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	80	434	1165	2176	434	1165	2176
14926	TP53	tumor protein p53	74	89	167	417	89	167	417
5242	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	34	56	56	78	56	56	78
5153	FBXW7	F-box and WD repeat domain containing 7	46	50	53	68	50	53	68
11060	POLE	polymerase (DNA directed), epsilon	47	39	42	60	39	42	60
11230	PPP2R1A	protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform	30	37	48	77	37	48	77
15262	TTN	titin	524	35	53	103	35	53	103

+ Geneset Analyses

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 69. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_ns_s	p	q
1	ARFPATHWAY	Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest.	ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1	16	ABL1(8), CDKN2A(2), E2F1(9), MDM2(4), MYC(8), PIK3CA(172), PIK3R1(100), POLR1A(16), POLR1B(16), POLR1C(2), POLR1D(3), RAC1(1), RB1(26), TBX2(2), TP53(74), TWIST1(1)	7247552	444	223	300	50	87	115	119	6	99	18	3.94e-10	<1.00e-15	<3.99e-14
2	MTORPATHWAY	Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation.	AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2	21	AKT1(4), EIF4A1(5), EIF4A2(9), EIF4B(7), EIF4E(2), EIF4G1(15), EIF4G2(7), EIF4G3(24), FKBP1A(1), MKNK1(3), PDK2(5), PDPK1(3), PIK3CA(172), PIK3R1(100), PPP2CA(6), PTEN(227), RPS6(7), RPS6KB1(5), TSC1(13), TSC2(15)	10458408	630	218	417	44	90	141	126	38	191	44	<1.00e-15	<1.00e-15	<3.99e-14
3	IGF1MTORPATHWAY	Growth factor IGF-1 activates AKT, Gsk3-beta, and mTOR to promote muscle hypertrophy.	AKT1, EIF2B5, EIF2S1, EIF2S2, EIF2S3, EIF4E, EIF4EBP1, FRAP1, GSK3B, IGF1, IGF1R, INPPL1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1	19	AKT1(4), EIF2B5(5), EIF2S1(2), EIF2S2(9), EIF2S3(6), EIF4E(2), GSK3B(13), IGF1(5), IGF1R(13), INPPL1(19), PDK2(5), PDPK1(3), PIK3CA(172), PIK3R1(100), PPP2CA(6), PTEN(227), RPS6(7), RPS6KB1(5)	7335096	603	217	388	46	79	131	117	40	194	42	<1.00e-15	<1.00e-15	<3.99e-14
4	SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES	Genes related to the insulin receptor pathway	AKT1, AKT2, AKT3, BRD4, CAP1, CBL, CDC42, CDKN2A, F2RL2, FLOT1, FLOT2, FOXO1A, GRB2, GSK3A, GSK3B, IGFBP1, INPPL1, IRS1, IRS2, IRS4, LNPEP, MAPK1, MAPK3, PARD3, PARD6A, PDK1, PIK3CA, PIK3CD, PIK3R1, PPYR1, PSCD3, PTEN, PTPN1, RAF1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SERPINB6, SFN, SHC1, SLC2A4, SORBS1, SOS1, SOS2, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ	47	AKT1(4), AKT2(6), AKT3(11), BRD4(10), CAP1(7), CBL(12), CDC42(4), CDKN2A(2), F2RL2(2), FLOT2(2), GRB2(3), GSK3A(10), GSK3B(13), IGFBP1(4), INPPL1(19), IRS1(13), IRS4(21), LNPEP(10), MAPK1(2), MAPK3(3), PARD3(19), PDK1(2), PIK3CA(172), PIK3CD(12), PIK3R1(100), PPYR1(8), PTEN(227), PTPN1(5), RAF1(8), RPS6KA1(1), RPS6KA2(14), RPS6KA3(19), RPS6KB1(5), SERPINB6(3), SHC1(7), SLC2A4(9), SORBS1(18), SOS1(13), SOS2(17), YWHAE(4), YWHAG(3), YWHAH(3), YWHAQ(1), YWHAZ(1)	21082232	829	217	605	120	160	197	174	40	214	44	5.04e-12	<1.00e-15	<3.99e-14
5	SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES	Genes related to PIP3 signaling in B lymphocytes	AKT1, AKT2, AKT3, BCR, BTK, CD19, CDKN2A, DAPP1, FLOT1, FLOT2, FOXO3A, GAB1, ITPR1, ITPR2, ITPR3, LYN, NR0B2, P101-PI3K, PDK1, PHF11, PIK3CA, PITX2, PLCG2, PPP1R13B, PREX1, PSCD3, PTEN, PTPRC, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SAG, SYK, TEC, VAV1	32	AKT1(4), AKT2(6), AKT3(11), BCR(6), BTK(12), CD19(4), CDKN2A(2), DAPP1(9), FLOT2(2), GAB1(8), ITPR1(36), ITPR2(35), ITPR3(21), LYN(9), NR0B2(2), PDK1(2), PHF11(5), PIK3CA(172), PITX2(12), PLCG2(29), PPP1R13B(9), PREX1(25), PTEN(227), PTPRC(17), RPS6KA1(1), RPS6KA2(14), RPS6KA3(19), RPS6KB1(5), SAG(10), SYK(4), TEC(8), VAV1(12)	20541344	738	212	540	128	147	231	144	38	149	29	5.04e-10	<1.00e-15	<3.99e-14
6	ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY	The phosphoinositide-3 kinase pathway produces the lipid second messenger PIP3 and regulates cell growth, survival, and movement.	A1BG, AKT1, AKT2, AKT3, BAD, BTK, CDKN2A, CSL4, DAF, DAPP1, FOXO1A, GRB2, GSK3A, GSK3B, IARS, IGFBP1, INPP5D, P14, PDK1, PIK3CA, PPP1R13B, PSCD3, PTEN, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SFN, SHC1, SOS1, SOS2, TEC, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ	33	A1BG(3), AKT1(4), AKT2(6), AKT3(11), BAD(2), BTK(12), CDKN2A(2), DAPP1(9), GRB2(3), GSK3A(10), GSK3B(13), IARS(8), IGFBP1(4), INPP5D(9), PDK1(2), PIK3CA(172), PPP1R13B(9), PTEN(227), RPS6KA1(1), RPS6KA2(14), RPS6KA3(19), RPS6KB1(5), SHC1(7), SOS1(13), SOS2(17), TEC(8), YWHAE(4), YWHAG(3), YWHAH(3), YWHAQ(1), YWHAZ(1)	13352320	602	211	404	65	112	161	131	37	133	28	1.22e-15	<1.00e-15	<3.99e-14
7	GSK3PATHWAY	Bacterial lipopolysaccharide activates AKT to promote the survival and activation of macrophages and inhibits Gsk3-beta to promote beta-catenin accumulation in the nucleus.	AKT1, APC, AXIN1, CCND1, CD14, CTNNB1, DVL1, FZD1, GJA1, GNAI1, GSK3B, IRAK1, LBP, LEF1, LY96, MYD88, NFKB1, PDPK1, PIK3CA, PIK3R1, PPP2CA, PRKR, RELA, TIRAP, TLR4, TOLLIP, WNT1	26	AKT1(4), APC(56), AXIN1(9), CCND1(15), CD14(2), CTNNB1(80), DVL1(3), FZD1(3), GJA1(5), GNAI1(5), GSK3B(13), IRAK1(4), LBP(3), LEF1(9), LY96(4), MYD88(3), NFKB1(10), PDPK1(3), PIK3CA(172), PIK3R1(100), PPP2CA(6), RELA(6), TIRAP(2), TLR4(17), TOLLIP(1), WNT1(1)	11218032	536	210	356	58	77	201	122	6	110	20	9.76e-14	<1.00e-15	<3.99e-14
8	NFATPATHWAY	Cardiac hypertrophy is induced by NF-ATc4 and GATA4, which are stimulated through calcineurin activated by CaMK.	ACTA1, AGT, AKT1, CALM1, CALM2, CALM3, CALR, CAMK1, CAMK1G, CAMK4, CREBBP, CSNK1A1, CTF1, DTR, EDN1, ELSPBP1, F2, FGF2, FKBP1A, GATA4, GSK3B, HAND1, HAND2, HRAS, IGF1, LIF, MAP2K1, MAPK1, MAPK14, MAPK3, MAPK8, MEF2C, MYH2, NFATC1, NFATC2, NFATC3, NFATC4, NKX2-5, NPPA, PIK3CA, PIK3R1, PPP3CA, PPP3CB, PPP3CC, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, RAF1, RPS6KB1, SYT1	52	ACTA1(5), AGT(8), AKT1(4), CALM1(2), CALM2(4), CALR(3), CAMK1(2), CAMK1G(5), CAMK4(5), CREBBP(32), CSNK1A1(4), EDN1(4), ELSPBP1(5), F2(8), FKBP1A(1), GATA4(3), GSK3B(13), HAND1(6), HRAS(1), IGF1(5), LIF(3), MAP2K1(2), MAPK1(2), MAPK14(4), MAPK3(3), MAPK8(10), MEF2C(11), MYH2(43), NFATC1(10), NFATC2(13), NFATC3(12), NFATC4(7), NKX2-5(2), NPPA(2), PIK3CA(172), PIK3R1(100), PPP3CA(4), PPP3CB(5), PPP3CC(6), PRKACB(3), PRKACG(9), PRKAR1A(4), PRKAR1B(4), PRKAR2A(4), PRKAR2B(3), RAF1(8), RPS6KB1(5), SYT1(4)	18646128	575	207	445	97	126	176	137	5	113	18	3.38e-08	<1.00e-15	<3.99e-14
9	IL2RBPATHWAY	The beta subunit of the IL-2 receptor is required for IL-2 and IL-15 signal recognition and activates JAK kinase on ligand binding.	AKT1, BAD, BCL2, BCL2L1, CBL, CFLAR, CRKL, E2F1, FOS, GRB2, HRAS, IL2RA, IL2RB, IL2RG, IRS1, JAK1, JAK3, MAPK1, MAPK3, MYC, NMI, PIK3CA, PIK3R1, PPIA, PTPN6, RAF1, RPS6KB1, SHC1, SOCS1, SOCS3, SOS1, STAT5A, STAT5B, SYK, TNFRSF6, TNFSF6, ZNFN1A3	33	AKT1(4), BAD(2), BCL2L1(4), CBL(12), CFLAR(6), CRKL(6), E2F1(9), FOS(3), GRB2(3), HRAS(1), IL2RA(4), IL2RB(3), IL2RG(13), IRS1(13), JAK1(20), JAK3(10), MAPK1(2), MAPK3(3), MYC(8), NMI(3), PIK3CA(172), PIK3R1(100), PPIA(1), PTPN6(6), RAF1(8), RPS6KB1(5), SHC1(7), SOS1(13), STAT5A(5), STAT5B(7), SYK(4)	13344136	457	203	334	55	84	140	122	5	91	15	1.67e-10	<1.00e-15	<3.99e-14
10	AKTPATHWAY	Second messenger PIP3 promotes cell survival by activating the anti-apoptotic kinase AKT.	AKT1, BAD, CASP9, CHUK, FOXO1A, FOXO3A, GH1, GHR, HSPCA, MLLT7, NFKB1, NFKBIA, PDPK1, PIK3CA, PIK3R1, PPP2CA, RELA, TNFSF6, YWHAH	14	AKT1(4), BAD(2), CASP9(3), CHUK(8), GH1(3), GHR(8), NFKB1(10), NFKBIA(3), PDPK1(3), PIK3CA(172), PIK3R1(100), PPP2CA(6), RELA(6), YWHAH(3)	5298520	331	199	212	19	49	93	92	4	78	15	3.56e-13	<1.00e-15	<3.99e-14

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p_ns_s	p	q
1	HSA00627_1,4_DICHLOROBENZENE_DEGRADATION	Genes involved in 1,4-dichlorobenzene degradation	CMBL	1	CMBL(3)	187984	3	3	3	1	0	1	0	1	1	0	0.81	0.18	1
2	PEPIPATHWAY	Proepithelin (PEPI) induces epithelial cells to secrete IL-8, which promotes elastase secretion by neutrophils.	ELA1, ELA2, ELA2A, ELA2B, ELA3B, GRN, IL8, SLPI	3	GRN(5), IL8(3), SLPI(2)	635128	10	10	9	0	2	5	2	0	1	0	0.057	0.32	1
3	HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM	Genes involved in D-arginine and D-ornithine metabolism	DAO	1	DAO(8)	268832	8	6	8	1	2	4	2	0	0	0	0.3	0.33	1
4	TCRMOLECULE	T Cell Receptor and CD3 Complex	CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@	3	CD3D(6), CD3E(2), CD3G(3)	437720	11	7	11	1	1	7	0	0	3	0	0.18	0.41	1
5	LDLPATHWAY	Low density lipoproteins (LDL) are present in blood plasma, contain cholesterol and triglycerides, and contribute to atherogenic plaque formation.	ACAT1, CCL2, CSF1, IL6, LDLR, LPL	6	ACAT1(6), CSF1(6), IL6(5), LDLR(6), LPL(16)	1950272	39	23	39	7	10	15	9	0	5	0	0.057	0.42	1
6	IL17PATHWAY	Activated T cells secrete IL-17, which stimulates fibroblasts and other cells to secrete inflammatory and hematopoietic cytokines.	CD2, CD34, CD3D, CD3E, CD3G, CD3Z, CD4, CD58, CD8A, CSF3, IL17, IL3, IL6, IL8, KITLG, TRA@, TRB@	13	CD2(4), CD34(1), CD3D(6), CD3E(2), CD3G(3), CD4(6), CD58(2), CD8A(2), CSF3(1), IL3(2), IL6(5), IL8(3), KITLG(3)	2324752	40	27	40	9	6	20	4	0	10	0	0.18	0.42	1
7	P27PATHWAY	p27 blocks the G1/S transition by inhibiting the checkpoint kinase cdk2/cyclin E and is inhibited by cdk2-mediated ubiquitination.	CCNE1, CDK2, CDKN1B, CKS1B, CUL1, E2F1, NEDD8, RB1, RBX1, SKP1A, SKP2, TFDP1, UBE2M	12	CCNE1(6), CDK2(2), CDKN1B(7), CKS1B(1), CUL1(13), E2F1(9), RB1(26), RBX1(1), SKP2(7), TFDP1(13)	3255992	85	39	83	17	27	25	17	0	13	3	0.027	0.43	1
8	HSA00643_STYRENE_DEGRADATION	Genes involved in styrene degradation	FAH, GSTZ1, HGD	3	FAH(6), GSTZ1(5), HGD(4)	842456	15	12	15	2	5	4	4	0	2	0	0.11	0.48	1
9	HSA00031_INOSITOL_METABOLISM	Genes involved in inositol metabolism	ALDH6A1, TPI1	2	ALDH6A1(6), TPI1(2)	594208	8	7	8	1	0	3	1	0	4	0	0.28	0.56	1
10	SA_BONE_MORPHOGENETIC	Bone morphogenetic protein binds to its receptor to induce ectopic bone formation and promote development of the viscera.	BMP1, BMPR1A, BMPR1B, BMPR2, MADH1, MADH4, MADH6	4	BMP1(19), BMPR1A(5), BMPR1B(6), BMPR2(12)	2288296	42	24	42	5	13	15	7	2	5	0	0.026	0.58	1

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