Mutation Analysis (MutSig v2.0) - Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

Mutation Analysis (MutSig v2.0)

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C14F1P0F

- Overview

+ Introduction

- Summary

MAF used for this analysis:UCEC-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 32
Mutations seen in COSMIC: 1001
Significantly mutated genes in COSMIC territory: 46
Genes with clustered mutations (≤ 3 aa apart): 4304
Significantly mutated genesets: 68
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 211 blacklisted mutations: 184495
After removing 1932 noncoding mutations: 182563
After collapsing adjacent/redundant mutations: 182561

Mutation Filtering

Number of mutations before filtering: 182561
After removing 15927 mutations outside gene set: 166634
After removing 1021 mutations outside category set: 165613
After removing 27 "impossible" mutations in
gene-patient-category bins of zero coverage: 148638

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	1025
Frame_Shift_Ins	447
In_Frame_Del	686
In_Frame_Ins	130
Missense_Mutation	110554
Nonsense_Mutation	11525
Nonstop_Mutation	127
Silent	38550
Splice_Site	2569
Total	165613

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
*CpG->T	37482	363920417	0.0001	100	5.7	2.2
*Cp(A/C/T)->mut	48855	3147487610	0.000016	16	0.85	3.4
A->mut	23150	3458111551	6.7e-06	6.7	0.37	3.8
*CpG->(G/A)	1051	363920417	2.9e-06	2.9	0.16	2.7
indel+null	15642	6969519578	2.2e-06	2.2	0.12	NaN
double_null	866	6969519578	1.2e-07	0.12	0.0068	NaN
Total	127046	6969519578	0.000018	18	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_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: 32. 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_cons	p_joint	p	q
1	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	306286	228	161	134	5	20	29	21	33	98	27	<1.00e-15	3.7e-12	0.9	1e-06	<0.000	<0.000
2	FBXW7	F-box and WD repeat domain containing 7	638720	46	39	30	1	22	12	2	1	8	1	7.88e-15	0.00048	0.015	0.00081	2.22e-16	1.70e-12
3	SPOP	speckle-type POZ protein	287083	23	21	18	0	5	8	6	0	4	0	7.33e-15	0.0041	0.05	0.0015	4.44e-16	1.70e-12
4	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	813637	172	132	76	3	31	61	68	3	9	0	2.00e-15	2.1e-11	8e-07	0	<1.00e-15	<1.70e-12
5	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	581125	100	83	77	2	4	4	13	1	63	15	<1.00e-15	0.0021	0.58	0	<1.00e-15	<1.70e-12
6	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	592248	80	74	25	7	5	61	14	0	0	0	6.22e-15	0.0034	2e-07	0	<1.00e-15	<1.70e-12
7	TP53	tumor protein p53	317550	74	69	50	2	23	18	15	1	17	0	4.00e-15	2.1e-06	2.6e-06	0	<1.00e-15	<1.70e-12
8	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	175322	53	53	11	2	1	47	4	1	0	0	5.55e-15	0.0059	0.00019	0	<1.00e-15	<1.70e-12
9	PPP2R1A	protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform	434902	30	27	18	3	10	17	1	0	2	0	3.44e-14	0.0026	0.23	0	<1.00e-15	<1.70e-12
10	PRKAR1B	protein kinase, cAMP-dependent, regulatory, type I, beta	242642	4	4	4	3	2	0	0	1	1	0	0.987	0.8	0	0	<1.00e-15	<1.70e-12
11	CTCF	CCCTC-binding factor (zinc finger protein)	547098	49	45	39	1	8	4	7	0	27	3	3.00e-15	0.00095	0.1	0.021	2.44e-15	3.77e-12
12	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	687457	34	31	19	3	3	5	13	9	3	1	1.03e-14	0.0097	0.38	0.059	2.20e-14	3.11e-11
13	P2RY11	purinergic receptor P2Y, G-protein coupled, 11	4342	7	9	9	1	1	4	0	1	1	0	5.27e-14	0.19	NaN	NaN	5.27e-14	6.89e-11
14	ARID1A	AT rich interactive domain 1A (SWI-like)	1412380	93	83	78	5	2	7	5	1	64	14	3.33e-15	0.00015	0.88	1	1.14e-13	1.39e-10
15	CCND1	cyclin D1	154874	15	15	13	1	1	7	3	0	4	0	1.16e-11	0.083	0.28	0.001	4.00e-13	4.53e-10
16	CHD4	chromodomain helicase DNA binding protein 4	1452335	43	35	38	2	16	16	8	0	2	1	3.80e-11	0.0045	0.7	0.046	4.90e-11	5.20e-08
17	NFE2L2	nuclear factor (erythroid-derived 2)-like 2	446498	15	15	12	0	2	3	5	3	2	0	3.32e-08	0.018	0.039	0.000082	7.53e-11	7.52e-08
18	SOX17	SRY (sex determining region Y)-box 17	77226	7	7	3	0	0	6	0	0	1	0	5.85e-08	0.13	0.079	0.02	2.53e-08	2.39e-05
19	FOXA2	forkhead box A2	222670	13	12	13	1	1	3	3	0	6	0	2.59e-08	0.26	0.28	0.21	1.08e-07	9.68e-05
20	FAM9A	family with sequence similarity 9, member A	249932	20	14	20	1	2	12	1	0	4	1	1.06e-07	0.1	1	0.26	5.11e-07	0.000434
21	SMTNL2	smoothelin-like 2	189739	9	9	3	2	0	2	0	0	7	0	0.000887	0.37	0.67	0.000094	1.44e-06	0.00117
22	RBMX	RNA binding motif protein, X-linked	309438	14	13	8	0	1	4	2	0	7	0	4.37e-05	0.3	0.2	0.014	9.24e-06	0.00713
23	MAX	MYC associated factor X	205913	12	11	8	0	3	3	5	0	1	0	1.55e-05	0.05	0.017	0.048	1.13e-05	0.00831
24	ING1	inhibitor of growth family, member 1	255446	13	13	10	2	4	1	0	1	7	0	0.000678	0.082	0.082	0.0027	2.60e-05	0.0184
25	RPL14	ribosomal protein L14	165361	8	7	4	0	0	1	0	2	5	0	0.000172	0.36	0.95	0.016	3.85e-05	0.0252
26	ABI1	abl-interactor 1	390369	5	4	2	5	0	5	0	0	0	0	1.000	1	1	2.8e-06	3.86e-05	0.0252
27	DNER	delta/notch-like EGF repeat containing	485604	21	18	20	1	4	9	5	0	3	0	0.000229	0.011	0.0045	0.016	4.87e-05	0.0306
28	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	145328	9	9	6	2	1	4	3	0	1	0	0.000366	0.48	0.015	0.014	6.60e-05	0.0400
29	HPD	4-hydroxyphenylpyruvate dioxygenase	304730	7	7	3	0	0	0	1	0	6	0	0.0398	0.64	0.00056	0.00021	0.000104	0.0609
30	RASA1	RAS p21 protein activator (GTPase activating protein) 1	776972	30	22	28	3	5	9	4	0	11	1	0.000178	0.094	0.053	0.05	0.000113	0.0641
31	ZNF267	zinc finger protein 267	555952	22	16	19	1	10	5	3	1	3	0	2.07e-05	0.13	0.74	0.5	0.000130	0.0709
32	SGK1	serum/glucocorticoid regulated kinase 1	469608	16	15	14	3	2	5	1	1	7	0	0.000296	0.52	0.011	0.049	0.000177	0.0939
33	ARID5B	AT rich interactive domain 5B (MRF1-like)	886908	34	29	34	9	5	5	8	2	13	1	0.000104	0.57	0.98	0.17	0.000207	0.106
34	CYLC1	cylicin, basic protein of sperm head cytoskeleton 1	477704	27	18	27	2	0	16	7	0	4	0	2.77e-05	0.13	0.25	0.75	0.000245	0.122
35	DYRK1A	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	599522	12	12	11	1	5	2	1	1	2	1	0.00640	0.22	0.1	0.0033	0.000251	0.122

+ 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: 46. Number of genes displayed: 10

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	100	33	39	8184	111	0	0
2	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	53	52	49	12896	556649	0	0
3	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	172	220	150	54560	35669	0	0
4	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	80	138	67	34224	23813	0	0
5	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	34	51	24	12648	113	0	0
6	FBXW7	F-box and WD repeat domain containing 7	46	91	29	22568	852	0	0
7	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	228	767	219	190216	15125	0	0
8	TP53	tumor protein p53	74	356	72	88288	24186	0	0
9	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	9	33	6	8184	6490	1.3e-08	6.5e-06
10	RB1	retinoblastoma 1 (including osteosarcoma)	26	267	11	66216	30	6.6e-08	0.000029

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
10506	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	228	1624	2112	3003	1624	2112	3003
6933	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	53	669	993	1039	669	993	1039
9757	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	172	573	1075	1553	573	1075	1553
2897	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	80	434	1165	2176	434	1165	2176
13869	TP53	tumor protein p53	74	89	167	417	89	167	417
4594	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
4506	FBXW7	F-box and WD repeat domain containing 7	46	50	53	68	50	53	68
10022	POLE	polymerase (DNA directed), epsilon	47	39	42	60	39	42	60
10189	PPP2R1A	protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform	30	37	48	77	37	48	77
14206	TTN	titin	525	36	54	105	36	54	105

+ 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: 68. 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)	7080267	444	223	300	50	87	115	119	6	99	18	4.87e-10	<1.00e-15	<4.88e-14
2	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(18), PDK2(5), PDPK1(3), PIK3CA(172), PIK3R1(100), PPP2CA(6), PTEN(228), RPS6(7), RPS6KB1(5)	7138255	603	217	387	46	80	131	117	40	193	42	<1.00e-15	<1.00e-15	<4.88e-14
3	METPATHWAY	The hepatocyte growth factor receptor c-Met stimulates proliferation and alters cell motility and adhesion on binding the ligand HGF.	ACTA1, CRK, CRKL, DOCK1, ELK1, FOS, GAB1, GRB2, GRF2, HGF, HRAS, ITGA1, ITGB1, JUN, MAP2K1, MAP2K2, MAP4K1, MAPK1, MAPK3, MAPK8, MET, PAK1, PIK3CA, PIK3R1, PTEN, PTK2, PTK2B, PTPN11, PXN, RAF1, RAP1A, RAP1B, RASA1, SOS1, SRC, STAT3	35	ACTA1(5), CRK(2), CRKL(6), DOCK1(24), ELK1(3), FOS(3), GAB1(8), GRB2(3), HGF(14), HRAS(1), ITGA1(17), ITGB1(8), JUN(1), MAP2K1(2), MAP2K2(5), MAP4K1(11), MAPK1(2), MAPK3(3), MAPK8(10), MET(17), PAK1(3), PIK3CA(172), PIK3R1(100), PTEN(228), PTK2(12), PTK2B(16), PTPN11(8), PXN(6), RAF1(8), RAP1A(4), RAP1B(2), RASA1(30), SOS1(13), SRC(3), STAT3(10)	16563754	760	217	538	93	135	188	148	37	208	44	7.33e-15	<1.00e-15	<4.88e-14
4	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)	10634125	536	210	356	58	77	201	122	6	110	20	2.06e-13	<1.00e-15	<4.88e-14
5	PDGFPATHWAY	Platelet-derived growth factor (PDGF) receptor is phosphorylated on ligand binding and promotes cell proliferation.	CSNK2A1, ELK1, FOS, GRB2, HRAS, JAK1, JUN, MAP2K1, MAP2K4, MAP3K1, MAPK3, MAPK8, PDGFA, PDGFRA, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, RAF1, RASA1, SHC1, SOS1, SRF, STAT1, STAT3, STAT5A	26	CSNK2A1(9), ELK1(3), FOS(3), GRB2(3), HRAS(1), JAK1(20), JUN(1), MAP2K1(2), MAP2K4(9), MAP3K1(30), MAPK3(3), MAPK8(10), PDGFA(3), PDGFRA(24), PIK3CA(172), PIK3R1(100), PLCG1(12), PRKCA(10), RAF1(8), RASA1(30), SHC1(7), SOS1(13), SRF(3), STAT1(15), STAT3(10), STAT5A(5)	12730148	506	201	375	56	94	144	134	4	112	18	5.97e-12	<1.00e-15	<4.88e-14
6	IL7PATHWAY	IL-7 is required for B and T cell development and proliferation and may contribute to activation of VDJ recombination.	BCL2, CREBBP, EP300, FYN, IL2RG, IL7, IL7R, JAK1, JAK3, LCK, NMI, PIK3CA, PIK3R1, PTK2B, STAT5A, STAT5B	16	CREBBP(32), EP300(32), FYN(7), IL2RG(13), IL7(1), IL7R(12), JAK1(20), JAK3(10), LCK(5), NMI(3), PIK3CA(172), PIK3R1(100), PTK2B(16), STAT5A(5), STAT5B(7)	10213532	435	200	312	56	77	121	115	6	100	16	3.60e-08	<1.00e-15	<4.88e-14
7	GCRPATHWAY	Corticosteroids activate the glucocorticoid receptor (GR), which inhibits NF-kB and activates Annexin-1, thus inhibiting the inflammatory response.	ADRB2, AKT1, ANXA1, CALM1, CALM2, CALM3, CRN, GNAS, GNB1, GNGT1, HSPCA, NFKB1, NOS3, NPPA, NR3C1, PIK3CA, PIK3R1, RELA, SYT1	17	ADRB2(7), AKT1(4), ANXA1(5), CALM1(2), CALM2(4), GNAS(24), GNB1(2), GNGT1(1), NFKB1(10), NOS3(11), NPPA(2), NR3C1(18), PIK3CA(172), PIK3R1(100), RELA(6), SYT1(4)	6288912	372	197	249	26	79	99	91	4	84	15	9.69e-14	<1.00e-15	<4.88e-14
8	RASPATHWAY	Ras activation stimulates many signaling cascades, including PI3K/AKT activation to inhibit apoptosis.	AKT1, ARHA, BAD, BCL2L1, CASP9, CDC42, CHUK, ELK1, H2AFX, HRAS, MAP2K1, MAPK3, MLLT7, NFKB1, PIK3CA, PIK3R1, RAC1, RAF1, RALA, RALBP1, RALGDS, RELA, RHOA	21	AKT1(4), BAD(2), BCL2L1(4), CASP9(3), CDC42(4), CHUK(8), ELK1(3), H2AFX(1), HRAS(1), MAP2K1(2), MAPK3(3), NFKB1(10), PIK3CA(172), PIK3R1(100), RAC1(1), RAF1(8), RALA(6), RALBP1(6), RALGDS(9), RELA(6), RHOA(3)	6942603	356	197	235	28	56	106	95	4	78	17	4.18e-12	<1.00e-15	<4.88e-14
9	TPOPATHWAY	Thrombopoietin binds to its receptor and activates cell growth through the Erk and JNK MAP kinase pathways, protein kinase C, and JAK/STAT activation.	CSNK2A1, FOS, GRB2, HRAS, JAK2, JUN, MAP2K1, MAPK3, MPL, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, RAF1, RASA1, SHC1, SOS1, STAT1, STAT3, STAT5A, STAT5B, THPO	22	CSNK2A1(9), FOS(3), GRB2(3), HRAS(1), JAK2(17), JUN(1), MAP2K1(2), MAPK3(3), MPL(7), PIK3CA(172), PIK3R1(100), PLCG1(12), PRKCA(10), RAF1(8), RASA1(30), SHC1(7), SOS1(13), STAT1(15), STAT3(10), STAT5A(5), STAT5B(7), THPO(7)	10932923	442	196	313	50	83	126	118	4	92	19	2.33e-09	<1.00e-15	<4.88e-14
10	CDC42RACPATHWAY	PI3 kinase stimulates cell migration by activating cdc42, which activates ARP2/3, which in turn promotes formation of new actin fibers.	ACTR2, ACTR3, ARHA, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, CDC42, PAK1, PDGFRA, PIK3CA, PIK3R1, RAC1, WASL	14	ACTR2(6), ACTR3(1), ARPC1A(6), ARPC1B(5), ARPC2(1), ARPC3(1), ARPC4(1), CDC42(4), PAK1(3), PDGFRA(24), PIK3CA(172), PIK3R1(100), RAC1(1), WASL(9)	4979142	334	195	214	16	51	90	92	4	81	16	7.55e-15	<1.00e-15	<4.88e-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	p_ns_s	p	q
1	HSA00627_1,4_DICHLOROBENZENE_DEGRADATION	Genes involved in 1,4-dichlorobenzene degradation	CMBL	1	CMBL(3)	187727	3	3	3	1	0	1	0	1	1	0.81	0.21	1
2	TCAPOPTOSISPATHWAY	HIV infection upregulates Fas ligand in macrophages and CD4 in helper T cells, leading to widespread Fas-induced T cell apoptosis.	CCR5, CD28, CD3D, CD3E, CD3G, CD3Z, CD4, TNFRSF6, TNFSF6, TRA@, TRB@	6	CCR5(6), CD28(3), CD3D(6), CD3E(2), CD3G(3), CD4(6)	1210424	26	16	26	5	3	16	0	0	7	0.16	0.25	1
3	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)	572860	10	10	9	0	2	5	2	0	1	0.057	0.27	1
4	HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM	Genes involved in D-arginine and D-ornithine metabolism	DAO	1	DAO(8)	264662	8	6	8	1	2	4	2	0	0	0.3	0.35	1
5	TCRMOLECULE	T Cell Receptor and CD3 Complex	CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@	3	CD3D(6), CD3E(2), CD3G(3)	433293	11	7	11	1	1	7	0	0	3	0.18	0.44	1
6	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)	1914084	39	23	39	7	10	15	9	0	5	0.057	0.46	1
7	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)	2309359	40	27	40	9	6	20	4	0	10	0.18	0.48	1
8	HSA00643_STYRENE_DEGRADATION	Genes involved in styrene degradation	FAH, GSTZ1, HGD	3	FAH(6), GSTZ1(5), HGD(4)	822142	15	12	15	2	5	4	4	0	2	0.11	0.51	1
9	HSA00031_INOSITOL_METABOLISM	Genes involved in inositol metabolism	ALDH6A1, TPI1	2	ALDH6A1(6), TPI1(2)	582980	8	7	8	1	0	3	1	0	4	0.27	0.57	1
10	HSA00401_NOVOBIOCIN_BIOSYNTHESIS	Genes involved in novobiocin biosynthesis	GOT1, GOT2, TAT	3	GOT1(9), GOT2(3), TAT(7)	959929	19	13	19	2	7	6	5	1	0	0.088	0.64	1

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