Rectum Adenocarcinoma: Mutation Analysis (MutSig v2.0)<BR>(primary solid tumor cohort)

Rectum Adenocarcinoma: Mutation Analysis (MutSig v2.0)
(primary solid tumor cohort)

Maintained by Dan DiCara (Broad Institute)

- Overview

+ Introduction

- Summary

MAF used for this analysis:READ-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 26
Mutations seen in COSMIC: 222
Significantly mutated genes in COSMIC territory: 10
Genes with clustered mutations (≤ 3 aa apart): 117
Significantly mutated genesets: 111
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 200 mutations outside gene set: 21478
After removing 172 mutations outside category set: 21306
After removing 2 "impossible" mutations in
gene-patient-category bins of zero coverage: 20932

- Results

+ Breakdown of Mutations by Type

type	count
De_novo_Start_InFrame	4
De_novo_Start_OutOfFrame	30
Frame_Shift_Del	151
Frame_Shift_Ins	155
In_Frame_Del	27
In_Frame_Ins	7
Missense_Mutation	14471
Nonsense_Mutation	1779
Nonstop_Mutation	6
Read-through	10
Silent	4628
Splice_Site	38
Total	21306

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate
*CpG->T	4919	99673101	0.000049	49	5.4
*Cp(A/C/T)->mut	6672	832257993	8e-06	8	0.88
A->mut	2743	908854391	3e-06	3	0.33
*CpG->(G/A)	135	99673101	1.4e-06	1.4	0.15
indel+null	2051	1840785523	1.1e-06	1.1	0.12
double_null	157	1840785523	8.5e-08	0.085	0.0094
Total	16677	1840785523	9.1e-06	9.1	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_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: 26. 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_cons	p_joint	p	q
1	TP53	tumor protein p53	79667	45	45	30	1	19	6	6	2	12	0	<1.00e-15	NaN	NaN	<1.00e-15	<1.72e-11
2	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	48604	38	38	8	0	0	36	1	0	1	0	2.78e-15	NaN	NaN	2.78e-15	1.72e-11
3	APC	adenomatous polyposis coli	576224	66	57	56	0	1	4	4	0	39	18	2.89e-15	NaN	NaN	2.89e-15	1.72e-11
4	SMAD4	SMAD family member 4	115264	8	8	6	0	2	3	3	0	0	0	8.09e-11	NaN	NaN	8.09e-11	3.62e-07
5	KIAA1804		162266	11	9	9	0	7	3	1	0	0	0	1.25e-08	NaN	NaN	1.25e-08	4.48e-05
6	FBXW7	F-box and WD repeat domain containing 7	177744	12	9	10	0	6	2	2	0	2	0	1.94e-08	NaN	NaN	1.94e-08	5.80e-05
7	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	119026	7	7	7	1	2	3	0	0	2	0	1.00e-07	NaN	NaN	1.00e-07	0.000238
8	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	40433	5	5	4	0	0	3	2	0	0	0	1.06e-07	NaN	NaN	1.06e-07	0.000238
9	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	194975	7	7	7	1	1	3	3	0	0	0	2.12e-07	NaN	NaN	2.12e-07	0.000421
10	OPCML	opioid binding protein/cell adhesion molecule-like	73709	6	6	6	1	1	3	0	0	2	0	2.84e-07	NaN	NaN	2.84e-07	0.000509
11	SPATA8	spermatogenesis associated 8	20140	3	3	3	0	0	0	3	0	0	0	4.18e-06	NaN	NaN	4.18e-06	0.00681
12	KRTAP5-5	keratin associated protein 5-5	34487	2	2	1	0	0	0	0	2	0	0	2.10e-05	NaN	NaN	2.10e-05	0.0280
13	SMAD2	SMAD family member 2	98964	5	5	5	0	0	3	1	0	1	0	2.16e-05	NaN	NaN	2.16e-05	0.0280
14	IL1RAPL2	interleukin 1 receptor accessory protein-like 2	139823	5	5	4	2	2	1	0	0	2	0	2.19e-05	NaN	NaN	2.19e-05	0.0280
15	CSMD1	CUB and Sushi multiple domains 1	392008	12	9	12	2	4	4	2	0	1	1	2.40e-05	NaN	NaN	2.40e-05	0.0287
16	LRRTM2	leucine rich repeat transmembrane neuronal 2	59242	5	4	5	1	1	1	2	1	0	0	3.53e-05	NaN	NaN	3.53e-05	0.0395
17	SGCB	sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)	64145	4	4	4	0	0	3	0	0	0	1	4.59e-05	NaN	NaN	4.59e-05	0.0462
18	GFRA1	GDNF family receptor alpha 1	86296	5	5	5	1	1	0	3	0	1	0	4.65e-05	NaN	NaN	4.65e-05	0.0462
19	CCBP2	chemokine binding protein 2	79700	5	5	5	0	1	2	2	0	0	0	5.02e-05	NaN	NaN	5.02e-05	0.0473
20	LPHN3	latrophilin 3	147364	7	6	7	3	3	3	1	0	0	0	5.89e-05	NaN	NaN	5.89e-05	0.0492
21	ZIM3	zinc finger, imprinted 3	98103	6	5	6	0	1	1	3	0	1	0	6.02e-05	NaN	NaN	6.02e-05	0.0492
22	MAP2K3	mitogen-activated protein kinase kinase 3	67262	4	4	4	0	1	1	1	1	0	0	6.05e-05	NaN	NaN	6.05e-05	0.0492
23	FAM123B	family with sequence similarity 123B	190503	8	6	8	1	0	2	1	0	5	0	8.10e-05	NaN	NaN	8.10e-05	0.0630
24	PCDHA13	protocadherin alpha 13	162857	8	6	8	0	3	1	2	1	1	0	9.74e-05	NaN	NaN	9.74e-05	0.0727
25	C4BPA	complement component 4 binding protein, alpha	126397	5	5	5	1	2	2	0	0	1	0	0.000108	NaN	NaN	0.000108	0.0776
26	CSMD3	CUB and Sushi multiple domains 3	787754	11	9	11	6	2	4	2	2	1	0	0.000139	NaN	NaN	0.000139	0.0956
27	KCNS2	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	80231	5	5	5	0	2	2	1	0	0	0	0.000161	NaN	NaN	0.000161	0.107
28	CASP14	caspase 14, apoptosis-related cysteine peptidase	51900	5	4	4	0	4	1	0	0	0	0	0.000185	NaN	NaN	0.000185	0.118
29	RBM10	RNA binding motif protein 10	160754	5	5	4	0	0	1	0	0	4	0	0.000212	NaN	NaN	0.000212	0.131
30	SLITRK1	SLIT and NTRK-like family, member 1	134633	6	5	6	0	2	1	2	0	1	0	0.000293	NaN	NaN	0.000293	0.170
31	OSBPL6	oxysterol binding protein-like 6	208053	5	5	5	0	1	2	0	2	0	0	0.000295	NaN	NaN	0.000295	0.170
32	DKK4	dickkopf homolog 4 (Xenopus laevis)	46838	3	3	3	0	1	1	1	0	0	0	0.000316	NaN	NaN	0.000316	0.177
33	LIFR	leukemia inhibitory factor receptor alpha	228178	5	5	5	2	0	2	1	1	1	0	0.000359	NaN	NaN	0.000359	0.195
34	SAMD9L	sterile alpha motif domain containing 9-like	327283	9	6	9	1	1	6	1	0	1	0	0.000419	NaN	NaN	0.000419	0.216
35	FAT4	FAT tumor suppressor homolog 4 (Drosophila)	968552	17	10	17	5	5	8	3	0	1	0	0.000429	NaN	NaN	0.000429	0.216

+ 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	52	37	3588	363199	1.6e-13	7.2e-10
2	TP53	tumor protein p53	45	824	45	56856	17987	1.6e-12	2.4e-09
3	APC	adenomatous polyposis coli	66	839	50	57891	1048	1.6e-12	2.4e-09
4	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	5	33	5	2277	5755	3.1e-11	3.5e-08
5	FBXW7	F-box and WD repeat domain containing 7	12	91	6	6279	329	4.5e-11	4.1e-08
6	SMAD4	SMAD family member 4	8	159	6	10971	39	1.2e-09	9.2e-07
7	KRTAP5-5	keratin associated protein 5-5	2	1	2	69	2	1.9e-07	0.00012
8	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	4	42	3	2898	6	3e-06	0.0017
9	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	7	220	4	15180	1382	0.000013	0.0067
10	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	20	18	2	1242	2	0.000063	0.028

+ Clustered Mutations

num	gene	desc	n	nmuts0	nmuts3	nmuts12	npairs0	npairs3	npairs12
3872	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	38	278	416	445	278	416	445
7547	TP53	tumor protein p53	45	37	61	105	37	61	105
392	APC	adenomatous polyposis coli	66	11	21	47	11	21	47
2614	FBXW7	F-box and WD repeat domain containing 7	12	6	6	6	6	6	6
4875	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	5	6	6	6	6	6	6
6841	SMAD4	SMAD family member 4	8	4	4	6	4	4	6
2361	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	4	3	3	3	3	3	3
3782	KIAA1804		11	2	6	7	2	6	7
3465	IL1RAPL2	interleukin 1 receptor accessory protein-like 2	5	1	3	3	1	3	3
2083	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: 111. 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	ST_GRANULE_CELL_SURVIVAL_PATHWAY	The survival and differentiation of granule cells in the brain is controlled by pro-growth PACAP and pro-apoptotic ceramides.	ADPRT, APC, ASAH1, CAMP, CASP3, CERK, CREB1, CREB3, CREB5, CXCL2, DAG1, EPHB2, FOS, GNAQ, IL8RB, ITPKA, ITPKB, JUN, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, PACAP	25	APC(66), CASP3(1), CREB3(1), CREB5(2), DAG1(1), EPHB2(1), FOS(1), GNAQ(1), MAP2K4(2), MAPK10(4), MAPK8(5), MAPK8IP3(1), MAPK9(2)	2754563	88	58	78	3	7	9	7	2	45	18	<1.00e-15	<8.74e-14
2	ST_MYOCYTE_AD_PATHWAY	Cardiac myocytes have a variety of adrenergic receptors that induce subtype-specific signaling effects.	ADRB1, AKT1, APC, ASAH1, BF, CAMP, CAV3, DAG1, DLG4, EPHB2, GAS, GNAI1, GNAQ, HTATIP, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, PITX2, PLB, PTX1, PTX3, RAC1, RHO, RYR1	23	ADRB1(1), APC(66), CAV3(1), DAG1(1), DLG4(1), EPHB2(1), GNAI1(1), GNAQ(1), ITPR1(8), ITPR2(6), ITPR3(1), KCNJ5(1), KCNJ9(1), RHO(1), RYR1(6)	4224359	97	57	87	9	14	15	6	0	43	19	<1.00e-15	<8.74e-14
3	TGFBPATHWAY	The TGF-beta receptor responds to ligand binding by activating the SMAD family of transcriptional regulations, commonly blocking cell growth.	APC, CDH1, CREBBP, EP300, MADH2, MADH3, MADH4, MADH7, MADHIP, MAP2K1, MAP3K7, MAP3K7IP1, MAPK3, SKIL, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2	13	APC(66), CDH1(1), CREBBP(4), EP300(2), MAP2K1(1), MAP3K7(2), MAPK3(1), SKIL(1), TGFB2(4), TGFBR1(3)	2554178	85	57	75	4	5	10	8	0	44	18	<1.00e-15	<8.74e-14
4	HSA04370_VEGF_SIGNALING_PATHWAY	Genes involved in VEGF signaling pathway	AKT1, AKT2, AKT3, BAD, CASP9, CDC42, CHP, HRAS, KDR, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPKAPK2, MAPKAPK3, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NOS3, NRAS, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCG1, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKCA, PRKCB1, PRKCG, PTGS2, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, SH2D2A, SHC2, SPHK1, SPHK2, SRC, VEGFA	69	AKT2(1), AKT3(1), CDC42(1), KDR(2), KRAS(38), MAP2K1(1), MAP2K2(1), MAPK13(1), MAPK3(1), NFATC1(1), NFATC2(2), NFATC3(1), NFATC4(1), NRAS(5), PIK3CA(7), PIK3CD(1), PIK3CG(2), PIK3R1(5), PIK3R3(4), PLA2G4A(3), PLA2G6(2), PLCG2(4), PPP3CA(2), PPP3CB(1), PPP3CC(1), PRKCA(2), PRKCG(2), PTGS2(1), RAF1(2), SH2D2A(1), SHC2(1), SPHK1(1)	6915053	99	50	68	19	27	50	10	0	10	2	<1.00e-15	<8.74e-14
5	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)	1828212	57	49	42	5	26	7	8	2	14	0	<1.00e-15	<8.74e-14
6	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)	924291	51	47	36	3	22	7	8	2	12	0	1.11e-15	8.74e-14
7	G1_TO_S_CELL_CYCLE_REACTOME		ATM, CCNA1, CCNB1, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNG2, CCNH, CDC25A, CDC45L, CDK2, CDK4, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CREB3, CREB3L1, CREB3L3, CREB3L4, CREBL1, CREBL1, TNXB, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, FLJ14001, GADD45A, GBA2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MNAT1, MYC, MYT1, NACA, NACA, FKSG17, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, POLA2, POLE, POLE2, PRIM1, PRIM2A, RB1, RBL1, RPA1, RPA2, RPA3, TFDP1, TFDP2, TP53, WEE1	63	ATM(10), CCNA1(2), CCNE2(1), CDK4(1), CDKN1B(2), CREB3(1), CREB3L3(2), E2F3(1), MCM3(2), MCM5(3), MCM6(1), MCM7(1), MYT1(5), PCNA(1), POLE(4), POLE2(1), RB1(3), RBL1(2), TNXB(3), TP53(45)	7068990	91	53	75	16	31	25	12	3	19	1	1.22e-15	8.74e-14
8	P53HYPOXIAPATHWAY	Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage.	ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53	18	ABCB1(5), ATM(10), CPB2(1), CSNK1D(1), FHL2(1), HIF1A(2), IGFBP3(2), MAPK8(5), TP53(45)	2001688	72	50	57	4	26	18	9	3	15	1	1.33e-15	8.74e-14
9	WNTPATHWAY	The Wnt glycoprotein binds to membrane-bound receptors such as Frizzled to activate a number of signaling pathways, including that of beta-catenin.	APC, AXIN1, BTRC, CCND1, CREBBP, CSNK1A1, CSNK1D, CSNK2A1, CTBP1, CTNNB1, DVL1, FRAT1, FZD1, GSK3B, HDAC1, MADH4, MAP3K7, MAP3K7IP1, MYC, NLK, PPARD, PPP2CA, TCF1, TLE1, WIF1, WNT1	21	APC(66), AXIN1(1), BTRC(3), CREBBP(4), CSNK1D(1), CTNNB1(4), FZD1(1), GSK3B(1), MAP3K7(2), PPARD(1)	2701685	84	58	74	4	8	9	8	0	41	18	1.44e-15	8.74e-14
10	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)	1820960	62	50	47	6	21	14	9	2	15	1	1.67e-15	8.74e-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	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)	837086	11	10	11	2	3	5	1	0	2	0	0.0014	0.3
2	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)	837086	11	10	11	2	3	5	1	0	2	0	0.0014	0.3
3	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)	908762	14	9	14	1	4	5	1	1	3	0	0.0014	0.3
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)	7933506	67	28	65	15	18	26	10	0	13	0	0.0046	0.65
5	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)	917313	10	9	10	4	4	1	3	1	1	0	0.0053	0.65
6	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)	607553	10	8	10	1	3	4	1	0	2	0	0.0071	0.7
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)	2322908	29	13	29	7	8	7	5	0	7	2	0.008	0.7
8	NEUROTRANSMITTERSPATHWAY	Biosynthesis of neurotransmitters	DBH, GAD1, HDC, PNMT, TH, TPH1	6	DBH(1), GAD1(2), HDC(5), TPH1(2)	572489	10	7	10	2	3	5	1	0	1	0	0.01	0.77
9	HSA00150_ANDROGEN_AND_ESTROGEN_METABOLISM	Genes involved in androgen and estrogen metabolism	AKR1C4, AKR1D1, ARSD, ARSE, CARM1, CYP11B1, CYP11B2, CYP19A1, HEMK1, HSD11B1, HSD11B2, HSD17B1, HSD17B12, HSD17B2, HSD17B3, HSD17B7, HSD17B8, HSD3B1, HSD3B2, LCMT1, LCMT2, METTL2B, METTL6, PRMT2, PRMT3, PRMT5, PRMT6, PRMT7, PRMT8, SRD5A1, SRD5A2, STS, SULT1E1, SULT2A1, SULT2B1, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT2A1, UGT2A3, UGT2B10, UGT2B11, UGT2B15, UGT2B17, UGT2B28, UGT2B4, UGT2B7, WBSCR22	53	AKR1C4(1), AKR1D1(1), CYP11B1(4), CYP19A1(3), HSD17B2(1), HSD17B3(1), HSD3B1(1), HSD3B2(1), LCMT1(2), METTL2B(1), METTL6(3), PRMT3(1), PRMT7(1), PRMT8(2), SRD5A2(1), STS(1), SULT1E1(1), SULT2A1(1), UGT1A4(1), UGT1A6(1), UGT1A8(1), UGT1A9(1), UGT2A3(2), UGT2B11(2), UGT2B17(3), UGT2B28(1), UGT2B4(1), UGT2B7(2)	4462401	42	18	42	9	9	19	6	1	7	0	0.012	0.77
10	HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM	Genes involved in D-arginine and D-ornithine metabolism	DAO	1	DAO(4)	73821	4	3	4	0	3	1	0	0	0	0	0.012	0.77

+ Methods & Data

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