Breast Invasive Carcinoma: Mutation Analysis (MutSig v2.0)<BR>(primary solid tumor cohort)

Breast Invasive Carcinoma: Mutation Analysis (MutSig v2.0)
(primary solid tumor cohort)

Maintained by Dan DiCara (Broad Institute)

- Overview

+ Introduction

- Summary

MAF used for this analysis:BRCA-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 39
Mutations seen in COSMIC: 500
Significantly mutated genes in COSMIC territory: 16
Genes with clustered mutations (≤ 3 aa apart): 269
Significantly mutated genesets: 117
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

Read 507 MAFs of type "WashU"
Total number of mutations in input MAFs: 33982
After removing 41 mutations outside chr1-24: 33941
After removing 190 blacklisted mutations: 33751
After removing 1624 noncoding mutations: 32127
After collapsing adjacent/redundant mutations: 31850

Mutation Filtering

Number of mutations before filtering: 31850
After removing 1508 mutations outside gene set: 30342
After removing 148 mutations outside category set: 30194

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	953
Frame_Shift_Ins	308
In_Frame_Del	370
In_Frame_Ins	69
Missense_Mutation	19234
Nonsense_Mutation	1397
Nonstop_Mutation	34
Silent	7245
Splice_Site	584
Total	30194

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
*CpG->T	3898	836685876	4.7e-06	4.7	3.2	2.1
*Cp(A/C/T)->T	4289	7060503801	6.1e-07	0.61	0.41	1.7
C->(G/A)	6945	7897189677	8.8e-07	0.88	0.6	4.8
A->mut	4096	7654859394	5.4e-07	0.54	0.36	3.9
indel+null	3662	15552049071	2.4e-07	0.24	0.16	NaN
double_null	59	15552049071	3.8e-09	0.0038	0.0026	NaN
Total	22949	15552049071	1.5e-06	1.5	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)->T
n3 = number of nonsilent mutations of type: C->(G/A)
n4 = number of nonsilent mutations of type: A->mut
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: 39. 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	TP53	tumor protein p53	649467	187	184	113	3	29	23	23	39	73	0	<1.00e-15	3.33e-15	NaN	NaN	<1.00e-15	<9.14e-12
2	CDH1	cadherin 1, type 1, E-cadherin (epithelial)	1347099	33	33	30	1	0	3	1	0	29	0	<1.00e-15	0.0312	NaN	NaN	<1.00e-15	<9.14e-12
3	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	1666509	194	178	32	3	3	70	8	105	8	0	1.78e-15	<1.00e-15	NaN	NaN	1.78e-15	1.01e-11
4	MAP2K4	mitogen-activated protein kinase kinase 4	570375	20	20	19	0	3	2	2	1	12	0	2.22e-15	0.0346	NaN	NaN	2.22e-15	1.01e-11
5	MAP3K1	mitogen-activated protein kinase kinase kinase 1	2095431	46	38	45	3	0	0	2	5	24	15	3.44e-15	0.271	NaN	NaN	3.44e-15	1.13e-11
6	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	630708	18	18	17	1	0	2	1	3	12	0	4.22e-15	0.225	NaN	NaN	4.22e-15	1.13e-11
7	GATA3	GATA binding protein 3	574431	56	54	34	1	0	1	0	3	51	1	4.33e-15	0.519	NaN	NaN	4.33e-15	1.13e-11
8	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	632736	17	17	16	0	1	0	2	2	11	1	1.01e-14	0.181	NaN	NaN	1.01e-14	2.31e-11
9	MLL3	myeloid/lymphoid or mixed-lineage leukemia 3	7571538	37	36	37	1	0	8	3	3	23	0	5.28e-13	0.0486	NaN	NaN	5.28e-13	1.07e-09
10	TBX3	T-box 3 (ulnar mammary syndrome)	709800	13	13	13	0	0	2	1	0	10	0	1.90e-11	0.176	NaN	NaN	1.90e-11	3.48e-08
11	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	1196520	14	14	13	1	0	2	2	1	9	0	6.84e-11	0.610	NaN	NaN	6.84e-11	1.14e-07
12	CBFB	core-binding factor, beta subunit	246909	8	8	8	1	0	4	0	1	3	0	1.13e-10	0.339	NaN	NaN	1.13e-10	1.72e-07
13	AKT1	v-akt murine thymoma viral oncogene homolog 1	757965	12	12	2	1	0	11	0	1	0	0	3.12e-10	0.00521	NaN	NaN	3.12e-10	4.39e-07
14	TBL1XR1	transducin (beta)-like 1 X-linked receptor 1	811707	8	8	7	0	0	0	1	1	4	2	7.10e-07	0.445	NaN	NaN	7.10e-07	0.000928
15	CTCF	CCCTC-binding factor (zinc finger protein)	1127568	13	13	11	2	1	1	2	2	7	0	1.21e-06	0.494	NaN	NaN	1.21e-06	0.00147
16	NCOR1	nuclear receptor co-repressor 1	3804021	17	17	17	1	0	1	1	1	13	1	2.45e-06	0.128	NaN	NaN	2.45e-06	0.00280
17	FOXA1	forkhead box A1	603330	8	8	7	0	1	3	2	1	1	0	4.03e-06	0.0502	NaN	NaN	4.03e-06	0.00434
18	AFF2	AF4/FMR2 family, member 2	2066025	13	13	13	1	2	1	6	1	3	0	4.60e-06	0.235	NaN	NaN	4.60e-06	0.00468
19	VASN	vasorin	348309	6	6	3	0	0	0	1	4	1	0	5.49e-06	0.384	NaN	NaN	5.49e-06	0.00528
20	ZFP36L1	zinc finger protein 36, C3H type-like 1	519675	7	7	7	0	0	1	1	1	4	0	8.17e-06	0.305	NaN	NaN	8.17e-06	0.00747
21	RB1	retinoblastoma 1 (including osteosarcoma)	1394250	10	9	10	0	0	0	0	2	8	0	2.02e-05	0.302	NaN	NaN	2.02e-05	0.0176
22	C1orf65	chromosome 1 open reading frame 65	581529	7	7	5	0	1	4	1	1	0	0	2.22e-05	0.0373	NaN	NaN	2.22e-05	0.0185
23	CDKN1B	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	272259	5	5	4	0	0	0	0	0	5	0	2.44e-05	0.673	NaN	NaN	2.44e-05	0.0194
24	GPS2	G protein pathway suppressor 2	518661	6	6	6	1	0	0	0	0	6	0	3.59e-05	0.921	NaN	NaN	3.59e-05	0.0273
25	NEK5	NIMA (never in mitosis gene a)-related kinase 5	1078896	8	8	8	0	1	0	4	2	1	0	5.36e-05	0.184	NaN	NaN	5.36e-05	0.0392
26	MYB	v-myb myeloblastosis viral oncogene homolog (avian)	1177761	8	8	8	0	1	1	1	1	4	0	6.49e-05	0.214	NaN	NaN	6.49e-05	0.0456
27	OR5I1	olfactory receptor, family 5, subfamily I, member 1	480636	5	5	5	0	1	2	1	1	0	0	8.10e-05	0.139	NaN	NaN	8.10e-05	0.0549
28	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	358449	4	4	3	0	0	0	3	0	1	0	9.56e-05	0.773	NaN	NaN	9.56e-05	0.0624
29	UBC	ubiquitin C	978003	7	7	7	0	1	0	3	1	2	0	9.99e-05	0.276	NaN	NaN	9.99e-05	0.0630
30	SYCE1L	synaptonemal complex central element protein 1-like	238797	4	4	3	0	1	0	2	1	0	0	0.000116	0.361	NaN	NaN	0.000116	0.0687
31	HLA-DRB1	major histocompatibility complex, class II, DR beta 1	265161	4	4	4	1	0	0	1	2	1	0	0.000119	0.592	NaN	NaN	0.000119	0.0687
32	DCAF4L2	DDB1 and CUL4 associated factor 4-like 2	604344	7	7	7	0	4	2	1	0	0	0	0.000122	0.0583	NaN	NaN	0.000122	0.0687
33	SF3B1	splicing factor 3b, subunit 1, 155kDa	2047773	10	10	6	0	0	1	0	8	1	0	0.000124	0.0496	NaN	NaN	0.000124	0.0687
34	AVPI1	arginine vasopressin-induced 1	186069	4	4	3	0	1	0	3	0	0	0	0.000129	0.434	NaN	NaN	0.000129	0.0695
35	ATP10B	ATPase, class V, type 10B	2268318	12	12	12	1	3	2	4	2	1	0	0.000136	0.122	NaN	NaN	0.000136	0.0711

+ 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: 16. Number of genes displayed: 10

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	194	220	184	111540	113646	0	0
2	TP53	tumor protein p53	187	356	180	180492	37514	0	0
3	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	14	33	7	16731	8	1.7e-13	1.9e-10
4	GATA3	GATA binding protein 3	56	34	21	17238	155	1.7e-13	1.9e-10
5	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	18	178	14	90246	54	7.9e-13	6.2e-10
6	CDH1	cadherin 1, type 1, E-cadherin (epithelial)	33	185	15	93795	27	8.2e-13	6.2e-10
7	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	8	42	6	21294	44	1.5e-12	9.7e-10
8	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	17	767	17	388869	712	2.2e-12	1.2e-09
9	PTPN22	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	8	5	2	2535	2	7e-06	0.0035
10	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	4	51	3	25857	15	9e-06	0.0039

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
6931	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	194	4345	5558	5984	4345	5558	5984
9396	TP53	tumor protein p53	187	237	643	1330	237	643	1330
311	AKT1	v-akt murine thymoma viral oncogene homolog 1	12	55	55	55	55	55	55
8154	SF3B1	splicing factor 3b, subunit 1, 155kDa	10	10	10	10	10	10	10
6273	OBSCN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	27	7	7	8	7	7	8
9852	VASN	vasorin	6	6	6	6	6	6	6
1752	CDH1	cadherin 1, type 1, E-cadherin (epithelial)	33	5	5	6	5	5	6
2269	CTCF	CCCTC-binding factor (zinc finger protein)	13	3	7	7	3	7	7
3001	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	8	3	3	4	3	3	4
8761	SSPO	SCO-spondin homolog (Bos taurus)	15	3	3	4	3	3	4

+ 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: 117. 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	HSA04620_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY	Genes involved in Toll-like receptor signaling pathway	AKT1, AKT2, AKT3, CASP8, CCL3, CCL4, CCL5, CD14, CD40, CD80, CD86, CHUK, CXCL10, CXCL11, CXCL9, FADD, FOS, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IKBKB, IKBKE, IKBKG, IL12A, IL12B, IL1B, IL6, IL8, IRAK1, IRAK4, IRF3, IRF5, IRF7, JUN, LBP, LY96, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6, MAP2K7, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK8, MAPK9, MYD88, NFKB1, NFKB2, NFKBIA, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, RAC1, RELA, RIPK1, SPP1, STAT1, TBK1, TICAM1, TICAM2, TIRAP, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TNF, TOLLIP, TRAF3, TRAF6	99	AKT1(12), AKT2(1), AKT3(3), CASP8(3), CD14(1), CD40(1), CD86(2), IFNA1(1), IFNA10(1), IFNA13(1), IFNA14(2), IFNA16(1), IFNA2(2), IFNA4(1), IFNA7(1), IFNAR1(1), IFNAR2(1), IFNB1(1), IKBKB(3), IKBKE(1), IL12A(1), IL12B(1), IL6(2), IRAK1(1), IRAK4(2), IRF3(2), JUN(1), LBP(1), MAP2K1(1), MAP2K2(1), MAP2K3(1), MAP2K4(20), MAP2K7(1), MAP3K7(1), MAP3K8(2), MAPK1(1), MAPK10(1), MAPK14(1), MAPK3(1), MAPK8(2), NFKB1(1), NFKB2(3), NFKBIA(1), PIK3CA(194), PIK3CB(4), PIK3CG(2), PIK3R1(14), PIK3R3(1), RELA(1), RIPK1(3), SPP1(2), STAT1(1), TBK1(1), TICAM1(2), TIRAP(2), TLR1(1), TLR2(1), TLR3(1), TLR4(8), TLR5(1), TLR7(5), TLR8(3), TLR9(1), TRAF3(1), TRAF6(2)	67859415	340	267	165	40	20	108	32	126	53	1	1.50e-13	<1.00e-15	<1.81e-14
2	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	AKT1(12), ATF2(2), DLD(1), DUSP10(1), DUSP4(1), GAB1(1), GCK(2), IL1R1(1), JUN(1), MAP2K4(20), MAP2K5(2), MAP2K7(1), MAP3K1(46), MAP3K10(4), MAP3K11(1), MAP3K12(2), MAP3K13(5), MAP3K4(4), MAP3K5(2), MAP3K7(1), MAP3K9(3), MAPK10(1), MAPK8(2), MYEF2(2), NFATC3(3), NR2C2(1), PAPPA(4), SHC1(1), TP53(187), TRAF6(2), ZAK(1)	38087868	317	263	230	20	42	46	38	51	125	15	1.34e-13	<1.00e-15	<1.81e-14
3	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), BAK1(1), BID(4), CASP2(3), CASP6(2), CASP8(3), FAS(1), FASLG(1), JUN(1), MAP2K4(20), MAP3K1(46), MAPK10(1), MDM2(2), MYC(1), NFKB1(1), NFKBIA(1), PARP1(1), PRF1(2), RELA(1), RIPK1(3), TNFRSF1A(1), TP53(187), TRAF1(1)	27872325	285	245	209	14	39	34	33	47	117	15	4.00e-15	<1.00e-15	<1.81e-14
4	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(12), BCR(1), CRKL(1), GRB2(1), JAK2(5), JUN(1), MAP2K1(1), MAP2K4(20), MAP3K1(46), MAPK3(1), MAPK8(2), MYC(1), PIK3CA(194), PIK3R1(14), RAF1(1), SOS1(4), STAT1(1), STAT5A(3), STAT5B(4)	20923890	313	241	138	12	12	89	17	117	63	15	<1.00e-15	<1.00e-15	<1.81e-14
5	ST_B_CELL_ANTIGEN_RECEPTOR	B cell receptors bind antigens and promote B cell activation.	AKT1, AKT2, AKT3, BAD, BCR, BLNK, BTK, CD19, CSK, DAG1, EPHB2, GRB2, ITPKA, ITPKB, LYN, MAP2K1, MAP2K2, MAPK1, NFAT5, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIE, NFKBIL1, NFKBIL2, PAG, PI3, PIK3CA, PIK3CD, PIK3R1, PLCG2, PPP1R13B, RAF1, SERPINA4, SHC1, SOS1, SOS2, SYK, VAV1	38	AKT1(12), AKT2(1), AKT3(3), BAD(1), BCR(1), BLNK(1), BTK(3), CD19(2), DAG1(1), EPHB2(2), GRB2(1), ITPKA(1), ITPKB(8), LYN(4), MAP2K1(1), MAP2K2(1), MAPK1(1), NFAT5(3), NFKB1(1), NFKB2(3), NFKBIA(1), NFKBIE(1), PI3(1), PIK3CA(194), PIK3R1(14), PLCG2(2), PPP1R13B(2), RAF1(1), SERPINA4(3), SHC1(1), SOS1(4), SOS2(2), SYK(2), VAV1(2)	39742716	281	240	108	15	18	96	25	115	26	1	<1.00e-15	<1.00e-15	<1.81e-14
6	HSA04115_P53_SIGNALING_PATHWAY	Genes involved in p53 signaling pathway	APAF1, ATM, ATR, BAI1, BAX, BBC3, BID, CASP3, CASP8, CASP9, CCNB1, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNG1, CCNG2, CD82, CDC2, CDK2, CDK4, CDK6, CDKN1A, CDKN2A, CHEK1, CHEK2, CYCS, DDB2, EI24, FAS, GADD45A, GADD45B, GADD45G, GTSE1, IGF1, IGFBP3, LRDD, MDM2, MDM4, P53AIP1, PERP, PMAIP1, PPM1D, PTEN, RCHY1, RFWD2, RPRM, RRM2, RRM2B, SCOTIN, SERPINB5, SERPINE1, SESN1, SESN2, SESN3, SFN, SIAH1, STEAP3, THBS1, TNFRSF10B, TP53, TP53I3, TP73, TSC2, ZMAT3	65	APAF1(1), ATM(12), ATR(2), BAI1(7), BID(4), CASP8(3), CCNB1(2), CCNB3(6), CCND1(1), CCND3(3), CCNE1(1), CCNG2(2), CDK2(1), CDK6(1), CHEK2(2), DDB2(1), FAS(1), GTSE1(7), IGF1(1), IGFBP3(1), LRDD(1), MDM2(2), PERP(2), PTEN(17), RCHY1(1), RRM2(1), SERPINE1(2), SESN2(2), SIAH1(3), STEAP3(1), THBS1(4), TP53(187), TP53I3(1), TP73(1), TSC2(2)	49849761	286	232	211	15	45	34	39	60	106	2	4.00e-15	<1.00e-15	<1.81e-14
7	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	16	AKT1(12), CREB1(1), MAP2K1(1), MAP2K2(1), MAP2K3(1), MAP3K1(46), MAPK1(1), MAPK14(1), MAPK3(1), NFKB1(1), PIK3CA(194), PIK3R1(14), RB1(10), RELA(1), SP1(2)	15156765	287	230	113	12	6	86	14	116	50	15	<1.00e-15	<1.00e-15	<1.81e-14
8	PTENPATHWAY	PTEN suppresses AKT-induced cell proliferation and antagonizes the action of PI3K.	AKT1, BCAR1, CDKN1B, FOXO3A, GRB2, ILK, ITGB1, MAPK1, MAPK3, PDK2, PDPK1, PIK3CA, PIK3R1, PTEN, PTK2, SHC1, SOS1, TNFSF6	16	AKT1(12), CDKN1B(5), GRB2(1), ILK(2), ITGB1(2), MAPK1(1), MAPK3(1), PDK2(1), PIK3CA(194), PIK3R1(14), PTEN(17), PTK2(3), SHC1(1), SOS1(4)	14667003	258	226	83	10	7	89	15	111	35	1	<1.00e-15	<1.00e-15	<1.81e-14
9	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(12), EIF4A2(5), EIF4G1(1), EIF4G2(1), EIF4G3(2), GHR(2), IRS1(1), MAPK1(1), MAPK14(1), MAPK3(1), PABPC1(3), PDK2(1), PIK3CA(194), PIK3R1(14), PTEN(17)	21334560	256	225	82	14	7	89	17	109	33	1	<1.00e-15	<1.00e-15	<1.81e-14
10	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	AKT1(12), AKT2(1), AKT3(3), BAD(1), BTK(3), GRB2(1), GSK3A(1), IARS(6), INPP5D(3), PDK1(1), PIK3CA(194), PPP1R13B(2), PTEN(17), RPS6KA1(1), RPS6KA2(2), RPS6KA3(2), SHC1(1), SOS1(4), SOS2(2), TEC(1), YWHAB(1)	27296880	259	225	86	13	13	89	22	111	23	1	<1.00e-15	<1.00e-15	<1.81e-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	STILBENE_COUMARINE_AND_LIGNIN_BIOSYNTHESIS		EPX, GBA3, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, TPO, TYR	10	EPX(1), LPO(5), MPO(2), PRDX1(1), PRDX5(1), TPO(6), TYR(4)	7428057	20	20	20	2	6	2	5	3	4	0.067	0.018	1
2	ST_PAC1_RECEPTOR_PATHWAY	The signaling peptide PACAP binds to its receptor, PAC1R, which activates adenylyl cyclase and phospholipase C.	ASAH1, CAMP, DAG1, GAS, GNAQ, ITPKA, ITPKB, PACAP	6	ASAH1(1), DAG1(1), GNAQ(1), ITPKA(1), ITPKB(8)	4432701	12	12	12	0	2	1	3	4	2	0.04	0.022	1
3	HSA00601_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTOSERIES	Genes involved in glycosphingolipid biosynthesis - lactoseries	ABO, B3GALT1, B3GALT2, B3GALT5, B3GNT5, FUT1, FUT2, FUT3, ST3GAL3, ST3GAL4	10	ABO(4), B3GALT1(1), B3GALT2(1), B3GALT5(1), FUT2(2), FUT3(4), ST3GAL3(1), ST3GAL4(1)	5407662	15	15	14	2	4	5	2	2	2	0.05	0.033	1
4	CREMPATHWAY	The transcription factor CREM activates a post-meiotic transcriptional cascade culminating in spermatogenesis.	ADCY1, CREM, FHL5, FSHB, FSHR, GNAS, XPO1	7	ADCY1(3), CREM(2), FHL5(1), FSHR(4), GNAS(5), XPO1(3)	6833346	18	18	18	2	4	4	3	5	2	0.13	0.042	1
5	BLOOD_GROUP_GLYCOLIPID_BIOSYNTHESIS_LACTOSERIES		ABO, FUT1, FUT2, FUT3, FUT5, FUT6, SIAT6, ST3GAL3	7	ABO(4), FUT2(2), FUT3(4), FUT5(1), ST3GAL3(1)	3810105	12	12	11	2	4	3	1	2	2	0.096	0.064	1
6	HSA00940_PHENYLPROPANOID_BIOSYNTHESIS	Genes involved in phenylpropanoid biosynthesis	EPX, GBA, GBA3, LPO, MPO, PRDX6, TPO	7	EPX(1), LPO(5), MPO(2), TPO(6)	6402396	14	14	14	0	6	1	2	2	3	0.012	0.079	1
7	INOSITOL_METABOLISM		ALDH6A1, ALDOA, ALDOB, ALDOC, TPI1	5	ALDOA(4), ALDOB(2), TPI1(2)	2928939	8	8	8	0	0	4	3	0	1	0.051	0.086	1
8	METHIONINEPATHWAY	Catabolic Pathways for Methionine, Isoleucine, Threonine and Valine	BCKDHB, BCKDK, CBS, CTH, MUT	5	BCKDK(2), CBS(2), CTH(3), MUT(1)	3739125	8	8	8	0	1	1	1	1	4	0.14	0.12	1
9	METHANE_METABOLISM		ADH5, ATP6V0C, SHMT1, CAT, EPX, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, SHMT1, SHMT2, TPO	13	CAT(1), EPX(1), LPO(5), MPO(2), PRDX1(1), PRDX5(1), TPO(6)	9083412	17	17	17	1	7	1	2	3	4	0.036	0.15	1
10	SA_DIACYLGLYCEROL_SIGNALING	DAG (diacylglycerol) signaling activity	ESR1, ESR2, ITPKA, PDE1A, PDE1B, PLCB1, PLCB2, PRL, TRH, VIP	10	ESR1(2), ESR2(2), ITPKA(1), PDE1A(2), PDE1B(2), PLCB1(4), PLCB2(2), VIP(1)	8374626	16	16	16	2	2	6	3	3	2	0.12	0.15	1

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