Uterine Corpus Endometrioid Carcinoma: Mutation Analysis (MutSig v2.0)<BR>(primary solid tumor cohort)

Uterine Corpus Endometrioid Carcinoma: Mutation Analysis (MutSig v2.0)
(primary solid tumor cohort)

Maintained by Dan DiCara (Broad Institute)

- Overview

+ Introduction

- Summary

MAF used for this analysis:UCEC-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 36
Mutations seen in COSMIC: 1007
Significantly mutated genes in COSMIC territory: 47
Genes with clustered mutations (≤ 3 aa apart): 4496
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: 182433

Mutation Filtering

Number of mutations before filtering: 182433
After removing 8662 mutations outside gene set: 173771
After removing 1038 mutations outside category set: 172733

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	1059
Frame_Shift_Ins	461
In_Frame_Del	710
In_Frame_Ins	136
Missense_Mutation	115564
Nonsense_Mutation	11935
Nonstop_Mutation	138
Silent	40083
Splice_Site	2647
Total	172733

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
*CpG->T	38697	409266464	0.000095	95	5.4	2.1
*Cp(A/C/T)->mut	51438	3453658664	0.000015	15	0.85	3.3
A->mut	24335	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	16212	7607313944	2.1e-06	2.1	0.12	NaN
double_null	884	7607313944	1.2e-07	0.12	0.0067	NaN
Total	132650	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_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: 36. 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)	309504	227	161	134	5	19	29	21	33	98	27	<1.00e-15	4.9e-12	NaN	NaN	<1.00e-15	<3.66e-12
2	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	815176	172	132	76	3	31	61	68	3	9	0	<1.00e-15	2.1e-11	NaN	NaN	<1.00e-15	<3.66e-12
3	ARID1A	AT rich interactive domain 1A (SWI-like)	1428976	93	83	78	5	2	7	5	1	64	14	<1.00e-15	0.00014	NaN	NaN	<1.00e-15	<3.66e-12
4	TP53	tumor protein p53	317688	74	69	50	2	23	18	15	1	17	0	<1.00e-15	2.8e-06	NaN	NaN	<1.00e-15	<3.66e-12
5	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	<1.00e-15	0.0097	NaN	NaN	<1.00e-15	<3.66e-12
6	CTCF	CCCTC-binding factor (zinc finger protein)	551552	49	45	39	1	8	4	7	0	28	2	1.55e-15	0.00095	NaN	NaN	1.55e-15	4.74e-12
7	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	585280	100	83	77	2	4	4	13	1	63	15	1.89e-15	0.0021	NaN	NaN	1.89e-15	4.82e-12
8	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	175336	53	53	12	1	2	46	4	1	0	0	2.11e-15	0.0012	NaN	NaN	2.11e-15	4.82e-12
9	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	595696	80	74	25	7	5	61	14	0	0	0	4.11e-15	0.0034	NaN	NaN	4.11e-15	8.35e-12
10	FBXW7	F-box and WD repeat domain containing 7	640832	46	39	30	1	22	12	2	1	8	1	4.88e-15	0.00048	NaN	NaN	4.88e-15	8.93e-12
11	SPOP	speckle-type POZ protein	287928	23	21	18	0	5	8	6	0	4	0	1.28e-14	0.0041	NaN	NaN	1.28e-14	2.12e-11
12	PPP2R1A	protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform	453840	30	27	18	3	10	17	1	0	2	0	5.75e-14	0.0023	NaN	NaN	5.75e-14	8.76e-11
13	CHD4	chromodomain helicase DNA binding protein 4	1460720	43	35	38	2	16	16	8	0	2	1	1.45e-11	0.0046	NaN	NaN	1.45e-11	2.05e-08
14	P2RY11	purinergic receptor P2Y, G-protein coupled, 11	5704	9	9	9	3	3	4	0	1	1	0	2.14e-11	0.3	NaN	NaN	2.14e-11	2.79e-08
15	CCND1	cyclin D1	222952	15	15	13	1	1	7	3	0	4	0	7.28e-09	0.084	NaN	NaN	7.28e-09	8.87e-06
16	NFE2L2	nuclear factor (erythroid-derived 2)-like 2	449872	15	15	12	0	2	3	5	3	2	0	2.69e-08	0.016	NaN	NaN	2.69e-08	3.07e-05
17	FOXA2	forkhead box A2	227912	12	12	12	1	1	3	2	0	6	0	3.43e-08	0.27	NaN	NaN	3.43e-08	3.69e-05
18	FAM9A	family with sequence similarity 9, member A	255688	20	14	20	1	2	12	1	0	4	1	7.26e-08	0.096	NaN	NaN	7.26e-08	7.38e-05
19	SOX17	SRY (sex determining region Y)-box 17	91512	7	7	3	0	0	6	0	0	1	0	4.29e-07	0.15	NaN	NaN	4.29e-07	0.000412
20	ZNF267	zinc finger protein 267	557504	22	16	19	1	10	5	3	1	3	0	1.16e-05	0.13	NaN	NaN	1.16e-05	0.0105
21	MAX	MYC associated factor X	209064	12	11	8	0	3	3	5	0	1	0	1.20e-05	0.048	NaN	NaN	1.20e-05	0.0105
22	CYLC1	cylicin, basic protein of sperm head cytoskeleton 1	490048	27	18	27	2	0	16	7	0	4	0	2.06e-05	0.13	NaN	NaN	2.06e-05	0.0171
23	RBMX	RNA binding motif protein, X-linked	313224	14	13	8	0	1	4	2	0	7	0	2.77e-05	0.3	NaN	NaN	2.77e-05	0.0220
24	MORC4	MORC family CW-type zinc finger 4	685472	28	20	26	2	6	10	1	0	11	0	4.53e-05	0.083	NaN	NaN	4.53e-05	0.0340
25	OR4K2	olfactory receptor, family 4, subfamily K, member 2	235352	12	11	12	0	1	8	3	0	0	0	4.65e-05	0.028	NaN	NaN	4.65e-05	0.0340
26	ARID5B	AT rich interactive domain 5B (MRF1-like)	894536	34	29	34	9	5	5	8	2	13	1	5.47e-05	0.57	NaN	NaN	5.47e-05	0.0385
27	OR5D13	olfactory receptor, family 5, subfamily D, member 13	235104	10	10	9	0	2	4	2	0	2	0	6.69e-05	0.06	NaN	NaN	6.69e-05	0.0453
28	OR5AS1	olfactory receptor, family 5, subfamily AS, member 1	242296	12	10	12	1	1	7	4	0	0	0	6.96e-05	0.15	NaN	NaN	6.96e-05	0.0454
29	OR4A15	olfactory receptor, family 4, subfamily A, member 15	257424	16	13	16	1	1	10	5	0	0	0	0.000103	0.065	NaN	NaN	0.000103	0.0652
30	CSDE1	cold shock domain containing E1, RNA-binding	647528	32	21	28	3	12	9	5	1	5	0	0.000112	0.066	NaN	NaN	0.000112	0.0679
31	CTXN3	cortexin 3	62000	6	6	6	0	1	4	0	1	0	0	0.000117	0.21	NaN	NaN	0.000117	0.0679
32	PAPD4	PAP associated domain containing 4	374728	13	13	13	1	3	5	3	0	2	0	0.000119	0.26	NaN	NaN	0.000119	0.0679
33	RPL14	ribosomal protein L14	168392	8	7	4	0	0	1	0	2	5	0	0.000144	0.36	NaN	NaN	0.000144	0.0799
34	DNER	delta/notch-like EGF repeat containing	492528	21	18	20	1	4	9	5	0	3	0	0.000155	0.01	NaN	NaN	0.000155	0.0835
35	TAB3	TGF-beta activated kinase 1/MAP3K7 binding protein 3	537416	21	18	21	2	2	11	4	0	3	1	0.000171	0.18	NaN	NaN	0.000171	0.0877

+ 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	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)	227	767	218	190216	14940	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	1e-08	5.2e-06
10	RB1	retinoblastoma 1 (including osteosarcoma)	26	267	11	66216	30	4.2e-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
11544	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	226	1515	1989	2858	1515	1989	2858
7586	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	52	661	949	994	661	949	994
10787	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	172	573	1075	1553	573	1075	1553
3512	CTNNB1	catenin (cadherin-associated protein), beta 1, 88kDa	80	434	1165	2176	434	1165	2176
14922	TP53	tumor protein p53	74	89	167	417	89	167	417
5239	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
5150	FBXW7	F-box and WD repeat domain containing 7	46	50	53	68	50	53	68
11056	POLE	polymerase (DNA directed), epsilon	47	39	42	60	39	42	60
11226	PPP2R1A	protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform	30	37	48	77	37	48	77
15258	TTN	titin	523	35	53	102	35	53	102

+ 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)	7247552	444	223	300	50	87	115	119	6	99	18	3.94e-10	<1.00e-15	<4.11e-14
2	EIF4PATHWAY	The eIF-4F complex recognizes 5' mRNA caps, recruits RNA helicases, and maintains mRNA-ribosome bridging.	AKT1, EIF4A1, EIF4A2, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FRAP1, GHR, IRS1, MAPK1, MAPK14, MAPK3, MKNK1, PABPC1, PDK2, PDPK1, PIK3CA, PIK3R1, PRKCA, PRKCB1, PTEN, RPS6KB1	22	AKT1(4), EIF4A1(5), EIF4A2(9), EIF4E(2), EIF4G1(15), EIF4G2(7), EIF4G3(24), GHR(8), IRS1(13), MAPK1(2), MAPK14(4), MAPK3(3), MKNK1(3), PABPC1(11), PDK2(5), PDPK1(3), PIK3CA(172), PIK3R1(100), PRKCA(10), PTEN(227), RPS6KB1(5)	10435840	632	216	418	49	91	134	133	39	191	44	<1.00e-15	<1.00e-15	<4.11e-14
3	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	<4.11e-14
4	SA_PTEN_PATHWAY	PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate.	AKT1, AKT2, AKT3, BPNT1, GRB2, ILK, MAPK1, MAPK3, PDK1, PIK3CA, PIK3CD, PIP3-E, PTEN, PTK2B, RBL2, SHC1, SOS1	16	AKT1(4), AKT2(6), AKT3(11), BPNT1(3), GRB2(3), ILK(5), MAPK1(2), MAPK3(3), PDK1(2), PIK3CA(172), PIK3CD(12), PTEN(227), PTK2B(16), RBL2(19), SHC1(7), SOS1(13)	7530768	505	208	307	39	91	126	107	36	117	28	<1.00e-15	<1.00e-15	<4.11e-14
5	HDACPATHWAY	Myocyte enhancer factor MEF2 activates transcription of genes required for muscle cell differentiation and is inhibited by histone deacetylases.	AKT1, AVP, CABIN1, CALM1, CALM2, CALM3, CAMK1, CAMK1G, HDAC5, IGF1, IGF1R, INS, INSR, MAP2K6, MAPK14, MAPK7, MEF2A, MEF2B, MEF2C, MEF2D, MYOD1, NFATC1, NFATC2, PIK3CA, PIK3R1, PPP3CA, PPP3CB, PPP3CC, SYT1, YWHAH	28	AKT1(4), CABIN1(19), CALM1(2), CALM2(4), CAMK1(2), CAMK1G(5), HDAC5(12), IGF1(5), IGF1R(13), INS(3), INSR(18), MAP2K6(10), MAPK14(4), MAPK7(14), MEF2A(3), MEF2B(1), MEF2C(11), MEF2D(7), NFATC1(10), NFATC2(13), PIK3CA(172), PIK3R1(100), PPP3CA(4), PPP3CB(5), PPP3CC(6), SYT1(4), YWHAH(3)	12782416	454	202	331	71	109	116	116	8	90	15	1.34e-07	<1.00e-15	<4.11e-14
6	INSULINPATHWAY	Insulin regulates glucose levels via Ras-mediated transcriptional activation.	CSNK2A1, ELK1, FOS, GRB2, HRAS, INS, INSR, IRS1, JUN, MAP2K1, MAPK3, MAPK8, PIK3CA, PIK3R1, PTPN11, RAF1, RASA1, SHC1, SLC2A4, SOS1, SRF	21	CSNK2A1(9), ELK1(3), FOS(3), GRB2(3), HRAS(1), INS(3), INSR(18), IRS1(13), JUN(1), MAP2K1(2), MAPK3(3), MAPK8(10), PIK3CA(172), PIK3R1(100), PTPN11(8), RAF1(8), RASA1(30), SHC1(7), SLC2A4(9), SOS1(13), SRF(3)	9476328	419	202	292	39	82	118	108	5	90	16	2.40e-13	<1.00e-15	<4.11e-14
7	SIG_IL4RECEPTOR_IN_B_LYPHOCYTES	Genes related to IL4 rceptor signaling in B lymphocytes	AKT1, AKT2, AKT3, BAD, BCL2, GRB2, GSK3A, GSK3B, IL4R, IRS1, IRS2, JAK1, JAK3, MAP4K1, MAPK1, MAPK3, PDK1, PIK3CA, PIK3CD, PIK3R1, PPP1R13B, RAF1, SHC1, SOCS1, SOS1, SOS2, STAT6	25	AKT1(4), AKT2(6), AKT3(11), BAD(2), GRB2(3), GSK3A(10), GSK3B(13), IL4R(6), IRS1(13), JAK1(20), JAK3(10), MAP4K1(11), MAPK1(2), MAPK3(3), PDK1(2), PIK3CA(172), PIK3CD(12), PIK3R1(100), PPP1R13B(9), RAF1(8), SHC1(7), SOS1(13), SOS2(17), STAT6(10)	13137552	464	202	337	55	106	123	119	5	95	16	8.06e-11	<1.00e-15	<4.11e-14
8	GLEEVECPATHWAY	The drug Gleevec specifically targets the abnormal bcr-abl protein, an apoptosis inhibitor present in chronic myeloid leukemia.	AKT1, BCL2, BCR, CRKL, FOS, GRB2, HRAS, JAK2, JUN, MAP2K1, MAP2K4, MAP3K1, MAPK3, MAPK8, MYC, PIK3CA, PIK3R1, RAF1, SOS1, STAT1, STAT5A, STAT5B	22	AKT1(4), BCR(6), CRKL(6), FOS(3), GRB2(3), HRAS(1), JAK2(17), JUN(1), MAP2K1(2), MAP2K4(9), MAP3K1(30), MAPK3(3), MAPK8(10), MYC(8), PIK3CA(172), PIK3R1(100), RAF1(8), SOS1(13), STAT1(15), STAT5A(5), STAT5B(7)	10234960	423	199	298	39	75	122	113	4	90	19	9.63e-13	<1.00e-15	<4.11e-14
9	IGF1RPATHWAY	Insulin-like growth factor receptor IGF-1R promotes cell growth and inhibits apoptosis on binding of ligands IGF-1 and 2 via Ras activation and the AKT pathway.	AKT1, BAD, GRB2, HRAS, IGF1R, IRS1, MAP2K1, MAPK1, MAPK3, PIK3CA, PIK3R1, RAF1, SHC1, SOS1, YWHAH	15	AKT1(4), BAD(2), GRB2(3), HRAS(1), IGF1R(13), IRS1(13), MAP2K1(2), MAPK1(2), MAPK3(3), PIK3CA(172), PIK3R1(100), RAF1(8), SHC1(7), SOS1(13), YWHAH(3)	6997568	346	196	223	34	62	91	97	5	76	15	3.14e-09	<1.00e-15	<4.11e-14
10	NKCELLSPATHWAY	Natural killer (NK) lymphocytes are inhibited by MHC and activated by surface glycoproteins on tumor or virus-infected cells, which undergo perforin-mediated lysis.	B2M, HLA-A, IL18, ITGB1, KLRC1, KLRC2, KLRC3, KLRC4, KLRD1, LAT, MAP2K1, MAPK3, PAK1, PIK3CA, PIK3R1, PTK2B, PTPN6, RAC1, SYK, VAV1	20	B2M(3), HLA-A(1), IL18(2), ITGB1(8), KLRC1(7), KLRC2(3), KLRC3(1), KLRC4(5), KLRD1(3), MAP2K1(2), MAPK3(3), PAK1(3), PIK3CA(172), PIK3R1(100), PTK2B(16), PTPN6(6), RAC1(1), SYK(4), VAV1(12)	7058328	352	196	232	34	59	99	93	5	81	15	1.94e-09	<1.00e-15	<4.11e-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	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)	1218920	26	16	26	5	3	16	0	0	7	0	0.16	0.2	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)	635128	10	10	9	0	2	5	2	0	1	0	0.057	0.31	1
4	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	0.32	1
5	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
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)	1950272	39	23	39	7	10	15	9	0	5	0	0.057	0.41	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)	2324752	40	27	40	9	6	20	4	0	10	0	0.18	0.42	1
8	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	0.42	1
9	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
10	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

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