Mutation Analysis (MutSig v1.5) - Breast Invasive Carcinoma (Primary solid tumor)

Mutation Analysis (MutSig v1.5)

Breast Invasive Carcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v1.5). Broad Institute of MIT and Harvard. doi:10.7908/C1NV9G7X

- Overview

+ Introduction

- Summary

MAF used for this analysis:BRCA-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 74
Mutations seen in COSMIC: 727
Significantly mutated genes in COSMIC territory: 16
Genes with clustered mutations (≤ 3 aa apart): 270
Significantly mutated genesets: 123
Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing

Read 772 MAFs of type "WashU"
Total number of mutations in input MAFs: 47116
After removing 330 mutations outside chr1-24: 46786
After removing 559 blacklisted mutations: 46227
After removing 1703 noncoding mutations: 44524
After collapsing adjacent/redundant mutations: 44522

Mutation Filtering

Number of mutations before filtering: 44522
After removing 4090 mutations outside gene set: 40432
After removing 85 mutations outside category set: 40347
After removing 11 "impossible" mutations in
gene-patient-category bins of zero coverage: 36161

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	1246
Frame_Shift_Ins	704
In_Frame_Del	687
In_Frame_Ins	233
Missense_Mutation	25869
Nonsense_Mutation	1984
Nonstop_Mutation	38
Silent	8733
Splice_Site	853
Total	40347

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
*CpG->T	5166	1101604176	4.7e-06	4.7	3.2	2.2
*Cp(A/C/T)->T	5793	9664813395	6e-07	0.6	0.41	1.7
C->(G/A)	9406	10766417571	8.7e-07	0.87	0.59	4.9
A->mut	5498	10671091617	5.2e-07	0.52	0.35	3.8
indel+null	5666	21437509188	2.6e-07	0.26	0.18	NaN
double_null	79	21437509188	3.7e-09	0.0037	0.0025	NaN
Total	31608	21437509188	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_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
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: 74. 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_ns_s	p	q
1	GATA3	GATA binding protein 3	764273	84	81	50	1	0	1	1	4	77	1	0.473	<1.00e-15	<8.92e-12
2	CDH1	cadherin 1, type 1, E-cadherin (epithelial)	1998729	56	55	49	2	2	4	2	1	47	0	0.00243	1.55e-15	8.92e-12
3	TP53	tumor protein p53	974889	261	257	145	3	35	28	32	62	104	0	<1.00e-15	2.11e-15	8.92e-12
4	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	2526504	287	261	49	4	5	101	11	154	16	0	<1.00e-15	2.66e-15	8.92e-12
5	MAP3K1	mitogen-activated protein kinase kinase kinase 1	3179186	69	57	65	3	0	1	6	9	37	16	0.0748	3.77e-15	8.92e-12
6	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	794236	25	25	23	3	0	2	1	4	17	1	0.530	4.33e-15	8.92e-12
7	DSPP	dentin sialophosphoprotein	2697497	30	26	17	0	0	11	4	8	7	0	0.00226	5.00e-15	8.92e-12
8	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	956652	29	29	26	0	1	0	3	4	20	1	0.0931	5.55e-15	8.92e-12
9	NR1H2	nuclear receptor subfamily 1, group H, member 2	802056	18	18	5	0	2	0	0	1	15	0	0.390	5.55e-15	8.92e-12
10	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	1797680	21	21	20	1	0	3	2	3	13	0	0.352	5.88e-15	8.92e-12
11	MAP2K4	mitogen-activated protein kinase kinase 4	863577	32	32	28	0	3	2	5	2	20	0	0.0109	6.22e-15	8.92e-12
12	NCOA3	nuclear receptor coactivator 3	3363126	30	29	12	0	1	2	3	2	22	0	0.156	6.33e-15	8.92e-12
13	CBFB	core-binding factor, beta subunit	359167	16	16	16	1	0	4	3	4	5	0	0.142	6.99e-15	9.10e-12
14	AKT1	v-akt murine thymoma viral oncogene homolog 1	951700	19	19	2	1	0	18	0	1	0	0	7.29e-05	7.99e-15	9.66e-12
15	TBX3	T-box 3 (ulnar mammary syndrome)	991293	18	18	17	0	0	3	1	1	13	0	0.0585	1.21e-14	1.31e-11
16	MLL3	myeloid/lymphoid or mixed-lineage leukemia 3	11396219	58	56	56	1	2	10	6	4	34	2	0.00186	1.24e-14	1.31e-11
17	AOAH	acyloxyacyl hydrolase (neutrophil)	1514305	19	19	1	3	0	0	0	0	19	0	1.000	4.45e-14	4.43e-11
18	FOXA1	forkhead box A1	763360	15	15	15	0	1	3	2	4	5	0	0.0368	2.14e-13	2.01e-10
19	NCOR2	nuclear receptor co-repressor 2	3826500	29	29	7	1	1	0	2	0	26	0	0.731	2.89e-12	2.57e-09
20	MUC12	mucin 12, cell surface associated	6560731	50	44	38	8	12	7	13	9	8	1	0.0268	3.93e-10	3.32e-07
21	RBMX	RNA binding motif protein, X-linked	966111	13	13	2	1	0	0	0	0	13	0	1.000	5.28e-10	4.25e-07
22	MEF2A	myocyte enhancer factor 2A	1255054	14	14	3	0	0	0	0	1	13	0	0.745	2.04e-09	1.57e-06
23	NCOR1	nuclear receptor co-repressor 1	5748805	31	31	31	2	0	2	5	2	21	1	0.0529	4.67e-09	3.44e-06
24	ZNF384	zinc finger protein 384	1360722	14	14	1	1	0	0	0	0	14	0	1.000	9.65e-09	6.80e-06
25	ATN1	atrophin 1	2206723	18	17	9	1	0	5	2	0	11	0	0.248	2.55e-08	1.73e-05
26	ZFP36L1	zinc finger protein 36, C3H type-like 1	695039	10	10	10	0	0	1	1	1	7	0	0.306	4.99e-08	3.25e-05
27	KRTAP4-7	keratin associated protein 4-7	345100	7	7	2	1	0	0	1	6	0	0	0.638	1.56e-07	9.79e-05
28	RB1	retinoblastoma 1 (including osteosarcoma)	2081432	16	14	15	1	0	1	0	2	13	0	0.316	1.68e-07	0.000101
29	PHLDA1	pleckstrin homology-like domain, family A, member 1	522212	9	9	5	0	0	0	4	0	5	0	0.410	2.99e-07	0.000172
30	AKD1	adenylate kinase domain containing 1	4187803	19	19	10	0	0	2	4	0	13	0	0.273	3.06e-07	0.000172
31	CCDC144NL	coiled-coil domain containing 144 family, N-terminal like	495337	8	8	3	0	1	0	0	0	7	0	0.576	4.15e-07	0.000226
32	CDKN1B	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	389743	7	7	6	0	0	0	0	0	7	0	0.687	8.55e-07	0.000452
33	MUC20	mucin 20, cell surface associated	985055	10	10	6	0	4	4	1	1	0	0	0.0106	1.12e-06	0.000572
34	CASP8	caspase 8, apoptosis-related cysteine peptidase	1349654	10	10	10	0	2	2	1	3	2	0	0.0550	1.31e-06	0.000650
35	HIST1H3B	histone cluster 1, H3b	294971	7	7	7	1	1	2	2	0	2	0	0.262	1.69e-06	0.000816

+ 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	287	220	268	169840	161927	0	0
2	TP53	tumor protein p53	261	356	248	274832	47662	0	0
3	CDH1	cadherin 1, type 1, E-cadherin (epithelial)	56	185	23	142820	37	0	0
4	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	29	767	29	592124	1024	0	0
5	MAP2K4	mitogen-activated protein kinase kinase 4	32	15	6	11580	10	3.4e-13	3e-10
6	PIK3R1	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	21	33	12	25476	20	6.6e-13	4.2e-10
7	GATA3	GATA binding protein 3	84	34	32	26248	212	6.8e-13	4.2e-10
8	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)	12	42	8	32424	50	8.3e-13	4.5e-10
9	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	25	178	17	137416	57	3e-12	1.5e-09
10	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)	7	51	5	39372	21	5.2e-09	2.3e-06

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
7343	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	287	8908	11422	12316	8908	11422	12316
10236	TP53	tumor protein p53	261	439	1192	2731	439	1192	2731
353	AKT1	v-akt murine thymoma viral oncogene homolog 1	19	153	153	153	153	153	153
8775	SF3B1	splicing factor 3b, subunit 1, 155kDa	14	28	28	29	28	28	29
6263	MUC12	mucin 12, cell surface associated	50	26	32	39	26	32	39
2803	DSPP	dentin sialophosphoprotein	30	18	39	52	18	39	52
5343	KRTAP4-7	keratin associated protein 4-7	7	15	15	15	15	15	15
1688	CDH1	cadherin 1, type 1, E-cadherin (epithelial)	56	11	13	18	11	13	18
2672	DNAH14	dynein, axonemal, heavy chain 14	11	10	10	10	10	10	10
5269	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	6	10	10	10	10	10	10

+ 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: 123. 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	98	AKT1(19), AKT2(3), AKT3(4), CASP8(10), CD14(2), CD40(1), CD86(2), CHUK(1), IFNA1(1), IFNA10(1), IFNA13(1), IFNA14(2), IFNA16(1), IFNA17(1), IFNA2(3), IFNA21(1), IFNA4(1), IFNA6(2), IFNAR1(1), IFNAR2(1), IFNB1(1), IKBKB(4), IKBKE(2), IL12A(1), IL12B(1), IL6(2), IRAK1(2), IRAK4(3), IRF3(3), IRF5(1), IRF7(1), JUN(3), LBP(1), MAP2K1(1), MAP2K2(1), MAP2K3(2), MAP2K4(32), MAP2K6(1), MAP2K7(1), MAP3K7(1), MAP3K8(2), MAPK1(1), MAPK10(2), MAPK13(1), MAPK14(2), MAPK3(1), MAPK8(2), NFKB1(4), NFKB2(3), NFKBIA(1), PIK3CA(287), PIK3CB(6), PIK3CD(4), PIK3CG(3), PIK3R1(21), PIK3R3(2), RELA(1), RIPK1(3), SPP1(2), STAT1(1), TBK1(1), TICAM1(5), TIRAP(1), TLR1(1), TLR2(1), TLR3(5), TLR4(13), TLR5(2), TLR7(8), TLR8(3), TLR9(1), TRAF3(2), TRAF6(3)	97377478	517	400	253	42	27	160	56	187	85	2	<1.00e-15	<1.00e-15	<1.76e-14
2	HSA04012_ERBB_SIGNALING_PATHWAY	Genes involved in ErbB signaling pathway	ABL1, ABL2, AKT1, AKT2, AKT3, ARAF, AREG, BAD, BRAF, BTC, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CBL, CBLB, CBLC, CDKN1A, CDKN1B, CRK, CRKL, EGF, EGFR, EIF4EBP1, ELK1, ERBB2, ERBB3, ERBB4, EREG, FRAP1, GAB1, GRB2, GSK3B, HBEGF, HRAS, JUN, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MYC, NCK1, NCK2, NRAS, NRG1, NRG2, NRG3, NRG4, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, RAF1, RPS6KB1, RPS6KB2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SRC, STAT5A, STAT5B, TGFA	85	ABL1(5), ABL2(4), AKT1(19), AKT2(3), AKT3(4), ARAF(4), AREG(1), BRAF(3), BTC(1), CAMK2A(2), CAMK2D(4), CAMK2G(1), CBL(4), CBLB(10), CBLC(2), CDKN1B(7), CRK(1), CRKL(1), EGF(3), EGFR(5), ELK1(2), ERBB2(12), ERBB3(11), ERBB4(6), GAB1(2), GRB2(1), JUN(3), KRAS(6), MAP2K1(1), MAP2K2(1), MAP2K4(32), MAP2K7(1), MAPK1(1), MAPK10(2), MAPK3(1), MAPK8(2), MYC(1), NCK1(1), NCK2(1), NRAS(1), NRG1(2), NRG3(4), PAK1(2), PAK2(2), PAK3(2), PAK4(1), PAK6(1), PAK7(2), PIK3CA(287), PIK3CB(6), PIK3CD(4), PIK3CG(3), PIK3R1(21), PIK3R3(2), PLCG1(6), PLCG2(3), PRKCG(2), PTK2(5), RAF1(1), RPS6KB1(2), RPS6KB2(4), SHC1(1), SHC2(1), SHC3(1), SHC4(2), SOS1(4), SOS2(4), STAT5A(4), STAT5B(5), TGFA(1)	112604599	557	393	289	53	39	160	78	197	83	0	<1.00e-15	<1.00e-15	<1.76e-14
3	PPARAPATHWAY	Peroxisome proliferators regulate gene expression via PPAR/RXR heterodimers which bind to peroxisome-proliferator response elements (PPREs).	ACOX1, APOA1, APOA2, CD36, CITED2, CPT1B, CREBBP, DUSP1, DUT, EHHADH, EP300, FABP1, FAT, FRA8B, HSD17B4, HSPA1A, HSPCA, INS, JUN, LPL, MAPK1, MAPK3, ME1, MRPL11, MYC, NCOA1, NCOR1, NCOR2, NFKBIA, NOS2A, NR0B2, NR1H3, NR2F1, NRIP1, PDGFA, PIK3CA, PIK3R1, PPARA, PPARBP, PPARGC1, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PTGS2, RB1, RELA, RXRA, SP1, SRA1, STAT5A, STAT5B, TNF	49	ACOX1(2), CD36(1), CITED2(2), CPT1B(2), CREBBP(7), EHHADH(3), EP300(7), FABP1(1), HSD17B4(6), JUN(3), LPL(1), MAPK1(1), MAPK3(1), MRPL11(1), MYC(1), NCOA1(2), NCOR1(31), NCOR2(29), NFKBIA(1), NR0B2(2), NR2F1(1), NRIP1(3), PIK3CA(287), PIK3R1(21), PPARA(2), PRKACG(1), PRKAR1A(4), PRKAR2A(1), PRKAR2B(1), PTGS2(2), RB1(16), RELA(1), RXRA(1), SP1(3), SRA1(1), STAT5A(4), STAT5B(5)	68924350	458	361	195	30	20	120	40	172	105	1	<1.00e-15	<1.00e-15	<1.76e-14
4	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	40	APAF1(3), BAK1(2), BAX(2), BID(4), BIRC3(1), CASP2(3), CASP6(2), CASP7(1), CASP8(10), CASP9(1), FAS(1), FASLG(2), JUN(3), MAP2K4(32), MAP3K1(69), MAPK10(2), MCL1(1), MDM2(2), MYC(1), NFKB1(4), NFKBIA(1), PARP1(3), PRF1(2), RELA(1), RIPK1(3), TNFRSF1A(1), TP53(261), TRAF1(1)	40657541	419	357	294	14	51	46	53	78	175	16	<1.00e-15	<1.00e-15	<1.76e-14
5	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(19), BCR(3), CRKL(1), GRB2(1), JAK2(5), JUN(3), MAP2K1(1), MAP2K4(32), MAP3K1(69), MAPK3(1), MAPK8(2), MYC(1), PIK3CA(287), PIK3R1(21), RAF1(1), SOS1(4), STAT1(1), STAT5A(4), STAT5B(5)	30563652	461	355	197	16	15	129	31	173	97	16	<1.00e-15	<1.00e-15	<1.76e-14
6	TCRPATHWAY	T cell receptors bind to foreign peptides presented by MHC molecules and induce T cell activation.	CALM1, CALM2, CALM3, CD3D, CD3E, CD3G, CD3Z, ELK1, FOS, FYN, GRB2, HRAS, JUN, LAT, LCK, MAP2K1, MAP2K4, MAP3K1, MAPK3, MAPK8, NFATC1, NFATC2, NFATC3, NFATC4, NFKB1, NFKBIA, PIK3CA, PIK3R1, PLCG1, PPP3CA, PPP3CB, PPP3CC, PRKCA, PRKCB1, PTPN7, RAC1, RAF1, RASA1, RELA, SHC1, SOS1, SYT1, TRA@, TRB@, VAV1, ZAP70	42	CD3E(2), CD3G(2), ELK1(2), GRB2(1), JUN(3), LAT(1), LCK(1), MAP2K1(1), MAP2K4(32), MAP3K1(69), MAPK3(1), MAPK8(2), NFATC2(2), NFATC3(4), NFATC4(5), NFKB1(4), NFKBIA(1), PIK3CA(287), PIK3R1(21), PLCG1(6), PPP3CA(4), PPP3CB(3), PTPN7(2), RAF1(1), RASA1(2), RELA(1), SHC1(1), SOS1(4), VAV1(4), ZAP70(2)	52467488	471	355	224	29	20	123	40	176	96	16	<1.00e-15	<1.00e-15	<1.76e-14
7	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	AKT1(19), AKT2(3), AKT3(4), CASP9(1), KDR(2), KRAS(6), MAP2K1(1), MAP2K2(1), MAPK1(1), MAPK13(1), MAPK14(2), MAPK3(1), MAPKAPK2(1), MAPKAPK3(1), NFAT5(6), NFATC2(2), NFATC3(4), NFATC4(5), NOS3(3), NRAS(1), PIK3CA(287), PIK3CB(6), PIK3CD(4), PIK3CG(3), PIK3R1(21), PIK3R3(2), PLA2G12A(1), PLA2G2D(1), PLA2G2E(1), PLA2G2F(1), PLA2G3(2), PLA2G4A(7), PLA2G6(2), PLCG1(6), PLCG2(3), PPP3CA(4), PPP3CB(3), PPP3R1(1), PRKCG(2), PTGS2(2), PTK2(5), RAF1(1), SH2D2A(1), SHC2(1), SPHK2(2)	77057103	434	354	175	44	18	150	48	173	45	0	<1.00e-15	<1.00e-15	<1.76e-14
8	SIG_BCR_SIGNALING_PATHWAY	Members of the BCR signaling pathway	AKT1, AKT2, AKT3, BAD, BCL2, BCR, BLNK, BTK, CD19, CD22, CD81, CR2, CSK, DAG1, FLOT1, FLOT2, GRB2, GSK3A, GSK3B, INPP5D, ITPR1, ITPR2, ITPR3, LYN, MAP4K1, MAPK1, MAPK3, NFATC1, NFATC2, NR0B2, PDK1, PIK3CA, PIK3CD, PIK3R1, PLCG2, PPP1R13B, PPP3CA, PPP3CB, PPP3CC, PTPRC, RAF1, SHC1, SOS1, SOS2, SYK, VAV1	46	AKT1(19), AKT2(3), AKT3(4), BCR(3), BLNK(1), BTK(4), CD19(3), CD22(1), CR2(4), DAG1(1), FLOT1(1), FLOT2(2), GRB2(1), GSK3A(3), INPP5D(4), ITPR1(10), ITPR2(7), ITPR3(6), LYN(4), MAP4K1(4), MAPK1(1), MAPK3(1), NFATC2(2), NR0B2(2), PDK1(1), PIK3CA(287), PIK3CD(4), PIK3R1(21), PLCG2(3), PPP1R13B(3), PPP3CA(4), PPP3CB(3), PTPRC(3), RAF1(1), SHC1(1), SOS1(4), SOS2(4), SYK(2), VAV1(4)	80779691	436	353	180	38	23	147	45	179	42	0	<1.00e-15	<1.00e-15	<1.76e-14
9	HSA04150_MTOR_SIGNALING_PATHWAY	Genes involved in mTOR signaling pathway	AKT1, AKT2, AKT3, BRAF, CAB39, DDIT4, EIF4B, EIF4EBP1, FIGF, FRAP1, GBL, HIF1A, IGF1, INS, KIAA1303, LYK5, MAPK1, MAPK3, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PRKAA1, PRKAA2, RHEB, RICTOR, RPS6, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA6, RPS6KB1, RPS6KB2, STK11, TSC1, TSC2, ULK1, ULK2, ULK3, VEGFA, VEGFB, VEGFC	44	AKT1(19), AKT2(3), AKT3(4), BRAF(3), EIF4B(1), FIGF(2), HIF1A(1), IGF1(1), MAPK1(1), MAPK3(1), PIK3CA(287), PIK3CB(6), PIK3CD(4), PIK3CG(3), PIK3R1(21), PIK3R3(2), PRKAA1(1), PRKAA2(3), RHEB(1), RICTOR(3), RPS6(2), RPS6KA1(2), RPS6KA2(4), RPS6KA3(4), RPS6KA6(3), RPS6KB1(2), RPS6KB2(4), STK11(2), TSC1(4), TSC2(2), ULK1(1), ULK2(4), ULK3(2)	57150754	403	341	147	27	17	142	31	172	41	0	<1.00e-15	<1.00e-15	<1.76e-14
10	RAC1PATHWAY	Rac-1 is a Rho family G protein that stimulates formation of actin-dependent structures such as filopodia and lamellopodia.	ARFIP2, CDK5, CDK5R1, CFL1, CHN1, LIMK1, MAP3K1, MYL2, MYLK, NCF2, PAK1, PDGFRA, PIK3CA, PIK3R1, PLD1, PPP1R12B, RAC1, RALBP1, RPS6KB1, TRIO, VAV1, WASF1	22	CDK5(1), CHN1(3), LIMK1(4), MAP3K1(69), MYLK(8), NCF2(4), PAK1(2), PDGFRA(3), PIK3CA(287), PIK3R1(21), PLD1(5), PPP1R12B(1), RALBP1(1), RPS6KB1(2), TRIO(5), VAV1(4), WASF1(5)	39907968	425	336	182	27	10	119	35	175	70	16	<1.00e-15	<1.00e-15	<1.76e-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	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(3), CD34(2), CD3E(2), CD3G(2), CD4(4), CD58(1), CD8A(2), IL6(2), KITLG(3)	7120299	21	21	21	3	0	7	5	4	5	0.12	0.022	1
2	FBW7PATHWAY	Cyclin E interacts with cell cycle checkpoint kinase cdk2 to allow transcription of genes required for S phase, including transcription of additional cyclin E.	CCNE1, CDC34, CDK2, CUL1, E2F1, FBXW7, RB1, SKP1A, TFDP1	7	CCNE1(1), CDK2(1), CUL1(2), E2F1(4), FBXW7(6), TFDP1(2)	7497996	16	16	15	1	5	3	2	3	3	0.051	0.042	1
3	METHIONINEPATHWAY	Catabolic Pathways for Methionine, Isoleucine, Threonine and Valine	BCKDHB, BCKDK, CBS, CTH, MUT	5	BCKDK(5), CBS(2), CTH(3), MUT(3)	5387362	13	13	13	0	2	3	2	2	4	0.028	0.049	1
4	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(2), CD28(1), CD3E(2), CD3G(2), CD4(4)	3744423	11	11	11	2	1	4	2	1	3	0.31	0.094	1
5	TCRMOLECULE	T Cell Receptor and CD3 Complex	CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@	3	CD3E(2), CD3G(2)	1346070	4	4	4	0	0	3	0	1	0	0.21	0.12	1
6	IL18PATHWAY	Pro-inflammatory IL-18 is activated in macrophages by caspase-1 cleavage and, in conjunction with IL-12, stimulates Th1 cell differentiation.	CASP1, IFNG, IL12A, IL12B, IL18, IL2	6	CASP1(1), IFNG(2), IL12A(1), IL12B(1), IL18(1), IL2(1)	3530673	7	7	7	1	1	0	1	4	1	0.55	0.13	1
7	RABPATHWAY	Rab family GTPases regulate vesicle transport, endocytosis and exocytosis, and vesicle docking via interactions with the rabphilins.	ACTA1, MEL, RAB11A, RAB1A, RAB2, RAB27A, RAB3A, RAB4A, RAB5A, RAB6A, RAB7, RAB9A	9	ACTA1(2), RAB11A(2), RAB1A(2), RAB27A(1), RAB3A(2), RAB6A(1)	4901601	10	10	10	1	0	4	3	0	3	0.19	0.13	1
8	SA_PROGRAMMED_CELL_DEATH	Programmed cell death, or apoptosis, eliminates damaged or unneeded cells.	APAF1, BAD, BAK1, BAX, BCL10, BCL2, BCL2L1, BCL2L11, BID, CASP8AP2, CASP9, CES1	11	APAF1(3), BAK1(2), BAX(2), BCL10(1), BCL2L11(4), BID(4), CASP9(1), CES1(2)	8480554	19	19	18	2	4	5	4	2	4	0.13	0.17	1
9	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(2), FSHR(4), GNAS(5), XPO1(4)	10143105	20	20	19	2	4	4	4	5	3	0.1	0.18	1
10	ATMPATHWAY	The tumor-suppressing protein kinase ATM responds to radiation-induced DNA damage by blocking cell-cycle progression and activating DNA repair.	ABL1, ATM, BRCA1, CDKN1A, CHEK1, CHEK2, GADD45A, JUN, MAPK8, MDM2, MRE11A, NBS1, NFKB1, NFKBIA, RAD50, RAD51, RBBP8, RELA, TP53, TP73	18	ABL1(5), ATM(18), BRCA1(12), CHEK2(3), JUN(3), MAPK8(2), MDM2(2), MRE11A(2), NFKB1(4), NFKBIA(1), RAD50(2), RAD51(2), RBBP8(4), RELA(1), TP73(1)	31833859	62	57	62	5	7	10	15	9	21	0.0046	0.22	1

+ Methods & Data

Made with Nozzle