Rectum Adenocarcinoma: Mutation Analysis (MutSig v2.0)

Maintained by Dan DiCara (Broad Institute)

- Overview

+ Introduction

- Summary

MAF used for this analysis:READ.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 17
Mutations seen in COSMIC: 222
Significantly mutated genes in COSMIC territory: 10
Genes with clustered mutations (≤ 3 aa apart): 117
Significantly mutated genesets: 114
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

Read 38 MAFs of type "Broad"
Read 35 MAFs of type "Baylor"
Total number of mutations in input MAFs: 29413
After removing 257 invalidated mutations: 29156
After removing 200 noncoding mutations: 28956
After collapsing adjacent/redundant mutations: 21678

Mutation Filtering

Number of mutations before filtering: 21678
After removing 172 mutations outside gene set: 21506
After removing 172 mutations outside category set: 21334
After removing 5 "impossible" mutations in
gene-patient-category bins of zero coverage: 21329

- Results

+ Breakdown of Mutations by Type

type	count
De_novo_Start_InFrame	4
De_novo_Start_OutOfFrame	30
Frame_Shift_Del	153
Frame_Shift_Ins	155
In_Frame_Del	27
In_Frame_Ins	7
Missense_Mutation	14491
Nonsense_Mutation	1780
Nonstop_Mutation	6
Read-through	10
Silent	4633
Splice_Site	38
Total	21334

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate
*CpG->T	4922	112840423	0.000044	44	5.4
*Cp(A/C/T)->mut	6686	933772624	7.2e-06	7.2	0.88
A->mut	2744	1010264149	2.7e-06	2.7	0.33
*CpG->(G/A)	135	112840423	1.2e-06	1.2	0.15
indel+null	2054	2056877265	1e-06	1	0.12
double_null	157	2056877265	7.6e-08	0.076	0.0094
Total	16698	2056877265	8.1e-06	8.1	1

+ 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_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: 17. 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_ks	p_cons	p_joint	p	q
1	APC	adenomatous polyposis coli	592848	66	57	56	0	1	4	4	0	39	18	<1.00e-15	2e-07	0.9	0.000022	<0.000	<0.000
2	TP53	tumor protein p53	89473	45	45	30	1	19	6	6	2	12	0	3.66e-15	2e-07	2e-07	0	<1.00e-15	<4.50e-12
3	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	48783	38	38	8	0	0	36	1	0	1	0	1.89e-15	2e-07	0.00045	0	<1.00e-15	<4.50e-12
4	MUTYH	mutY homolog (E. coli)	118204	2	2	2	2	1	0	0	0	1	0	0.0426	0.25	0.022	0	<1.00e-15	<4.50e-12
5	SMAD4	SMAD family member 4	117507	8	8	6	0	2	3	3	0	0	0	4.55e-11	0.16	0.14	0.14	1.64e-10	5.91e-07
6	KIAA1804		165968	11	9	9	0	7	3	1	0	0	0	5.78e-09	0.025	0.011	0.011	1.50e-09	4.49e-06
7	FBXW7	F-box and WD repeat domain containing 7	178296	12	9	10	0	6	2	2	0	2	0	7.15e-09	0.072	0.059	0.058	9.39e-09	2.42e-05
8	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	40434	5	5	4	0	0	3	2	0	0	0	7.03e-08	0.012	0.42	0.023	3.44e-08	7.74e-05
9	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	140095	7	7	7	1	2	3	0	0	2	0	1.17e-07	0.061	0.033	0.032	7.65e-08	0.000153
10	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	226803	7	7	7	1	1	3	3	0	0	0	2.94e-07	0.11	0.39	0.15	7.77e-07	0.00140
11	OPCML	opioid binding protein/cell adhesion molecule-like	78039	6	6	6	1	1	3	0	0	2	0	2.42e-07	0.47	0.47	0.55	2.23e-06	0.00366
12	SMAD2	SMAD family member 2	99636	5	5	5	0	0	3	1	0	1	0	1.42e-05	0.012	0.3	0.018	4.04e-06	0.00606
13	SPATA8	spermatogenesis associated 8	22770	3	3	3	0	0	0	3	0	0	0	4.44e-06	0.098	0.48	0.14	9.21e-06	0.0128
14	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	261623	4	4	2	1	4	0	0	0	0	0	0.0238	0.000088	0.022	0.000049	1.70e-05	0.0219
15	IL1RAPL2	interleukin 1 receptor accessory protein-like 2	144969	5	5	4	2	2	1	0	0	2	0	1.40e-05	0.12	0.99	0.14	2.78e-05	0.0334
16	KRTAP5-5	keratin associated protein 5-5	38816	2	2	1	0	0	0	0	2	0	0	6.12e-05	0.08	0.0071	0.038	3.29e-05	0.0370
17	MARCKSL1	MARCKS-like 1	35451	2	2	1	0	0	0	0	0	2	0	0.00123	0.0017	0.17	0.0032	5.28e-05	0.0560
18	FAM123B	family with sequence similarity 123B	229757	8	6	8	1	0	2	1	0	5	0	0.000105	0.043	0.65	0.098	0.000128	0.128
19	ZIM3	zinc finger, imprinted 3	99015	6	5	6	0	1	1	3	0	1	0	4.61e-05	0.44	0.096	0.25	0.000144	0.134
20	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	161759	5	4	5	0	2	0	0	0	1	2	0.000441	0.023	0.59	0.027	0.000149	0.134
21	OSBPL6	oxysterol binding protein-like 6	208311	5	5	5	0	1	2	0	2	0	0	0.000176	0.22	0.059	0.076	0.000164	0.140
22	SGCB	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	65136	4	4	4	0	0	3	0	0	0	1	3.82e-05	0.28	0.67	0.4	0.000182	0.149
23	LIFR	leukemia inhibitory factor receptor alpha	232360	5	5	5	2	0	2	1	1	1	0	0.000225	0.22	0.051	0.075	0.000202	0.158
24	TLL2	tolloid-like 2	211905	3	3	2	2	2	0	1	0	0	0	0.0753	0.00014	0.18	0.00027	0.000240	0.173
25	CACNG7	calcium channel, voltage-dependent, gamma subunit 7	58512	3	3	3	0	2	0	0	1	0	0	0.000639	0.49	0.0036	0.032	0.000241	0.173
26	EPYC	epiphycan	68517	4	3	4	0	1	1	1	1	0	0	0.000465	0.033	0.45	0.047	0.000257	0.178
27	FAT4	FAT tumor suppressor homolog 4 (Drosophila)	1029673	17	10	17	5	5	8	3	0	1	0	0.000303	0.036	0.45	0.078	0.000275	0.184
28	CCBP2	chemokine binding protein 2	79971	5	5	5	0	1	2	2	0	0	0	3.51e-05	0.77	0.3	0.8	0.000320	0.199
29	FBXO15	F-box protein 15	92322	3	3	3	0	2	0	1	0	0	0	0.00232	0.0045	0.28	0.012	0.000321	0.199
30	CASP14	caspase 14, apoptosis-related cysteine peptidase	51957	5	4	4	0	4	1	0	0	0	0	0.000125	0.14	0.68	0.24	0.000344	0.201
31	HHEX	hematopoietically expressed homeobox	31954	2	2	2	0	0	1	1	0	0	0	0.0283	0.0025	0.35	0.0011	0.000355	0.201
32	CSMD3	CUB and Sushi multiple domains 3	791430	11	9	11	6	2	4	2	2	1	0	8.66e-05	0.42	0.17	0.36	0.000357	0.201
33	REEP2	receptor accessory protein 2	53463	2	2	2	0	0	0	2	0	0	0	0.0169	0.51	0.0015	0.002	0.000387	0.211
34	ZNF395	zinc finger protein 395	105838	2	2	1	0	0	0	1	0	1	0	0.0356	0.00066	0.77	0.0011	0.000452	0.238
35	SLITRK1	SLIT and NTRK-like family, member 1	144555	6	5	6	0	2	1	2	0	1	0	0.000237	0.14	0.57	0.18	0.000462	0.238

+ COSMIC analyses

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	38	51	37	3519	363199	1.6e-14	7.2e-11
2	TP53	tumor protein p53	45	823	45	56787	17987	1.7e-13	2.6e-10
3	APC	adenomatous polyposis coli	66	838	50	57822	1039	1.7e-13	2.6e-10
4	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	5	28	5	1932	5755	7.8e-12	8.8e-09
5	FBXW7	F-box and WD repeat domain containing 7	12	91	6	6279	329	2.3e-11	2.1e-08
6	SMAD4	SMAD family member 4	8	159	6	10971	39	6.4e-10	4.8e-07
7	KRTAP5-5	keratin associated protein 5-5	2	1	2	69	2	1.5e-07	0.0001
8	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	4	41	3	2829	6	2e-06	0.0011
9	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	7	184	4	12696	1382	4.3e-06	0.0022
10	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	20	18	2	1242	2	5e-05	0.023

+ Clustered Mutations

num	gene	desc	n	nmuts0	nmuts3	nmuts12	npairs0	npairs3	npairs12
3882	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	38	278	416	445	278	416	445
7563	TP53	tumor protein p53	45	37	61	105	37	61	105
393	APC	adenomatous polyposis coli	66	11	21	47	11	21	47
2623	FBXW7	F-box and WD repeat domain containing 7	12	6	6	6	6	6	6
4886	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	5	6	6	6	6	6	6
6854	SMAD4	SMAD family member 4	8	4	4	6	4	4	6
2368	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	4	3	3	3	3	3	3
3792	KIAA1804		11	2	6	7	2	6	7
3475	IL1RAPL2	interleukin 1 receptor accessory protein-like 2	5	1	3	3	1	3	3
2089	DNAH5	dynein, axonemal, heavy chain 5	19	1	2	2	1	2	2

+ 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: 114. 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	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	APC(66), AXIN1(1), AXIN2(2), BTRC(3), CACYBP(1), CAMK2D(1), CHD8(2), CREBBP(4), CTNNB1(4), CUL1(1), DAAM1(1), DAAM2(4), DKK1(2), DKK2(1), DKK4(3), DVL2(1), DVL3(2), EP300(2), FBXW11(1), FZD1(1), FZD10(2), FZD3(3), FZD4(1), FZD6(3), GSK3B(1), LRP6(7), MAP3K7(2), MAPK10(4), MAPK8(5), MAPK9(2), MMP7(2), NFATC1(1), NFATC2(2), NFATC3(1), NFATC4(1), PLCB3(1), PLCB4(1), PPARD(1), PPP2CB(2), PPP2R1B(1), PPP2R2B(2), PPP2R2C(1), PPP3CA(2), PPP3CB(1), PPP3CC(1), PRICKLE1(3), PRICKLE2(1), PRKACA(1), PRKACG(1), PRKCA(2), PRKCG(2), RBX1(1), RHOA(1), ROCK1(7), ROCK2(4), RUVBL1(2), SENP2(1), SFRP1(1), SFRP2(2), SFRP4(1), SMAD2(5), SMAD3(3), SMAD4(8), TBL1X(1), TBL1Y(1), TCF7(3), TCF7L2(7), TP53(45), WNT10B(1), WNT2(1), WNT2B(2), WNT6(1), WNT8A(1), WNT9B(1)	16648987	263	68	234	35	68	67	33	3	74	18	<1.00e-15	<6.22e-14
2	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	APC(66), AXIN1(1), CTNNB1(4), FZD1(1), GJA1(4), GNAI1(1), GSK3B(1), MYD88(1), NFKB1(3), PIK3CA(7), PIK3R1(5), TLR4(3)	3101261	97	60	87	4	12	15	10	0	40	20	<1.00e-15	<6.22e-14
3	ST_JNK_MAPK_PATHWAY	JNKs are MAP kinases regulated by several levels of kinases (MAPKK, MAPKKK) and phosphorylate transcription factors and regulatory proteins.	AKT1, ATF2, CDC42, DLD, DUSP10, DUSP4, DUSP8, GAB1, GADD45A, GCK, IL1R1, JUN, MAP2K4, MAP2K5, MAP2K7, MAP3K1, MAP3K10, MAP3K11, MAP3K12, MAP3K13, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K9, MAPK10, MAPK7, MAPK8, MAPK9, MYEF2, NFATC3, NR2C2, PAPPA, SHC1, TP53, TRAF6, ZAK	38	ATF2(1), CDC42(1), DLD(1), DUSP10(1), GCK(1), IL1R1(1), MAP2K4(2), MAP2K5(2), MAP3K1(2), MAP3K10(1), MAP3K12(2), MAP3K13(1), MAP3K2(1), MAP3K3(1), MAP3K4(3), MAP3K5(1), MAP3K7(2), MAP3K9(2), MAPK10(4), MAPK8(5), MAPK9(2), NFATC3(1), PAPPA(5), TP53(45), ZAK(2)	5206358	90	54	75	11	34	19	12	3	22	0	<1.00e-15	<6.22e-14
4	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(10), ATR(4), CCNA1(2), CDK4(1), CDKN1B(2), DHFR(1), GSK3B(1), RB1(3), TGFB2(4), TP53(45)	3112957	73	51	58	11	24	18	10	2	18	1	<1.00e-15	<6.22e-14
5	P53PATHWAY	p53 induces cell cycle arrest or apoptosis under conditions of DNA damage.	APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53	16	APAF1(1), ATM(10), CDK4(1), PCNA(1), RB1(3), TIMP3(1), TP53(45)	1905683	62	50	47	6	21	14	9	2	15	1	<1.00e-15	<6.22e-14
6	ATRBRCAPATHWAY	BRCA1 and 2 block cell cycle progression in response to DNA damage and promote double-stranded break repair; mutations induce breast cancer susceptibility.	ATM, ATR, BRCA1, BRCA2, CHEK1, CHEK2, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, HUS1, MRE11A, NBS1, RAD1, RAD17, RAD50, RAD51, RAD9A, TP53, TREX1	21	ATM(10), ATR(4), BRCA1(1), BRCA2(11), FANCA(2), FANCD2(4), FANCF(1), FANCG(2), MRE11A(5), RAD17(2), RAD50(6), TP53(45)	4587794	93	49	78	7	27	31	16	2	16	1	<1.00e-15	<6.22e-14
7	PMLPATHWAY	Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis.	CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1	13	CREBBP(4), DAXX(1), PAX3(2), PML(1), RB1(3), SIRT1(1), TP53(45)	1965067	57	49	42	5	26	7	8	2	14	0	<1.00e-15	<6.22e-14
8	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	CDK4(1), CDKN1B(2), PRB1(1), TP53(45)	831472	49	48	34	2	20	6	6	2	15	0	<1.00e-15	<6.22e-14
9	RNAPATHWAY	dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation.	CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53	9	CHUK(2), MAP3K14(1), NFKB1(3), TP53(45)	1059846	51	47	36	3	22	7	8	2	12	0	<1.00e-15	<6.22e-14
10	APOPTOSIS_GENMAPP		APAF1, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CASP2, CASP3, CASP6, CASP7, CASP8, CASP9, CYCS, FADD, FAS, FASLG, GZMB, IKBKG, JUN, MAP2K4, MAP3K1, MAP3K14, MAPK10, MCL1, MDM2, MYC, NFKB1, NFKBIA, PARP1, PRF1, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TNFSF10, TP53, TRADD, TRAF1, TRAF2	41	APAF1(1), BIRC2(2), BIRC3(5), CASP3(1), CASP6(1), FAS(2), GZMB(1), MAP2K4(2), MAP3K1(2), MAP3K14(1), MAPK10(4), NFKB1(3), TP53(45), TRAF1(1)	3868503	71	49	56	8	27	12	11	2	19	0	1.11e-15	6.22e-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	q
1	ERBB4PATHWAY	ErbB4 (aka HER4) is a receptor tyrosine kinase that binds neuregulins as well as members of the EGF family, which also target EGF receptors.	ADAM17, ERBB4, NRG2, NRG3, PRKCA, PRKCB1, PSEN1	6	ADAM17(1), ERBB4(5), NRG2(2), NRG3(4), PRKCA(2)	933406	14	9	14	1	4	5	1	1	3	0	0.00089	0.24
2	C21_STEROID_HORMONE_METABOLISM		AKR1C4, AKR1D1, CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD11B1, HSD11B2, HSD3B1, HSD3B2	11	AKR1C4(1), AKR1D1(1), CYP11A1(2), CYP11B1(4), CYP21A2(1), HSD3B1(1), HSD3B2(1)	921900	11	10	11	2	3	5	1	0	2	0	0.0012	0.24
3	HSA00140_C21_STEROID_HORMONE_METABOLISM	Genes involved in C21-steroid hormone metabolism	AKR1C4, AKR1D1, CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD11B1, HSD11B2, HSD3B1, HSD3B2	11	AKR1C4(1), AKR1D1(1), CYP11A1(2), CYP11B1(4), CYP21A2(1), HSD3B1(1), HSD3B2(1)	921900	11	10	11	2	3	5	1	0	2	0	0.0012	0.24
4	HSA00240_PYRIMIDINE_METABOLISM	Genes involved in pyrimidine metabolism	AICDA, AK3, CAD, CANT1, CDA, CMPK, CTPS, CTPS2, DCK, DCTD, DHODH, DPYD, DPYS, DTYMK, DUT, ECGF1, ENTPD1, ENTPD3, ENTPD4, ENTPD5, ENTPD6, ENTPD8, ITPA, NME1, NME2, NME4, NME6, NME7, NP, NT5C, NT5C1A, NT5C1B, NT5C2, NT5C3, NT5E, NT5M, NUDT2, PNPT1, POLA1, POLA2, POLD1, POLD2, POLD3, POLD4, POLE, POLE2, POLE3, POLE4, POLR1A, POLR1B, POLR1C, POLR1D, POLR2A, POLR2B, POLR2C, POLR2D, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J, POLR2K, POLR2L, POLR3A, POLR3B, POLR3G, POLR3GL, POLR3H, POLR3K, PRIM1, PRIM2, RFC5, RRM1, RRM2, RRM2B, TK1, TK2, TXNRD1, TXNRD2, TYMS, UCK1, UCK2, UMPS, UPB1, UPP1, UPP2, UPRT, ZNRD1	86	AICDA(1), CAD(1), CTPS(1), DCK(1), DHODH(1), DPYD(6), DPYS(1), DTYMK(1), ENTPD5(1), ENTPD6(1), NME6(1), NME7(2), NT5C1B(1), NT5C2(1), NT5E(1), PNPT1(5), POLA1(3), POLE(4), POLE2(1), POLR1A(3), POLR1B(2), POLR2B(3), POLR2K(1), POLR3A(4), POLR3B(5), POLR3K(1), PRIM2(3), RFC5(1), RRM1(1), TK2(1), TXNRD1(1), TXNRD2(1), TYMS(1), UMPS(1), UPB1(2), UPP2(1), UPRT(1)	8537733	67	28	65	15	18	26	10	0	13	0	0.0027	0.35
5	HCMVPATHWAY	Cytomegalovirus activates MAP kinase pathways in the host cell, inducing transcription of viral genes.	AKT1, CREB1, MAP2K1, MAP2K2, MAP2K3, MAP2K6, MAP3K1, MAPK1, MAPK14, MAPK3, NFKB1, PIK3CA, PIK3R1, RB1, RELA, SP1	15	MAP2K1(1), MAP2K2(1), MAP2K3(4), MAP2K6(1), MAP3K1(2), MAPK3(1), NFKB1(3), PIK3R1(5), RB1(3)	1817823	21	10	21	3	7	4	4	1	3	2	0.0028	0.35
6	CREMPATHWAY	The transcription factor CREM activates a post-meiotic transcriptional cascade culminating in spermatogenesis.	ADCY1, CREM, FHL5, FSHB, FSHR, GNAS, XPO1	7	ADCY1(4), FHL5(3), FSHB(1), FSHR(1), XPO1(1)	969112	10	9	10	4	4	1	3	1	1	0	0.0041	0.42
7	PAR1PATHWAY	Activated extracellular thrombin cleaves and activates the G-protein coupled receptors PAR1 and PAR4, which activate platelets.	ADCY1, ARHA, ARHGEF1, F2, F2R, F2RL3, GNA12, GNA13, GNAI1, GNAQ, GNB1, GNGT1, MAP3K7, PIK3CA, PIK3R1, PLCB1, PPP1R12B, PRKCA, PRKCB1, PTK2B, ROCK1	18	ADCY1(4), ARHGEF1(1), F2(1), GNAI1(1), GNAQ(1), GNGT1(1), MAP3K7(2), PIK3R1(5), PPP1R12B(4), PRKCA(2), ROCK1(7)	2455051	29	13	29	7	8	7	5	0	7	2	0.0052	0.45
8	GSPATHWAY	Activated G-protein coupled receptors stimulate cAMP production and thus activate protein kinase A, involved in a number of signal transduction pathways.	ADCY1, GNAS, GNB1, GNGT1, PRKACA, PRKAR1A	6	ADCY1(4), GNGT1(1), PRKACA(1), PRKAR1A(4)	661717	10	8	10	1	3	4	1	0	2	0	0.0063	0.48
9	HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM	Genes involved in D-arginine and D-ornithine metabolism	DAO	1	DAO(4)	74796	4	3	4	0	3	1	0	0	0	0	0.0084	0.54
10	NEUROTRANSMITTERSPATHWAY	Biosynthesis of neurotransmitters	DBH, GAD1, HDC, PNMT, TH, TPH1	6	DBH(1), GAD1(2), HDC(5), TPH1(2)	608603	10	7	10	2	3	5	1	0	1	0	0.0087	0.54

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