Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)

Cervical Squamous Cell 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 v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C10Z719T

- Overview

+ Introduction

- Summary

MAF used for this analysis:CESC-TP.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 4
Mutations seen in COSMIC: 35
Significantly mutated genes in COSMIC territory: 1
Significantly mutated genesets: 0

Mutation Preprocessing

Read 39 MAFs of type "Broad"
Total number of mutations in input MAFs: 10020
After removing 5 mutations outside chr1-24: 10015
After removing 261 blacklisted mutations: 9754
After removing 617 noncoding mutations: 9137

Mutation Filtering

Number of mutations before filtering: 9137
After removing 127 mutations outside gene set: 9010
After removing 21 mutations outside category set: 8989

- Results

+ Breakdown of Mutations by Type

type	count
Frame_Shift_Del	114
Frame_Shift_Ins	65
In_Frame_Del	52
In_Frame_Ins	15
Missense_Mutation	5620
Nonsense_Mutation	474
Nonstop_Mutation	11
Silent	2532
Splice_Site	93
Translation_Start_Site	13
Total	8989

+ Breakdown of Mutation Rates by Category Type

category	n	N	rate	rate_per_mb	relative_rate	exp_ns_s_ratio
Tp*C->(T/G)	3536	150569812	0.000023	23	4.1	3
(A/C/G)p*C->(T/G)	1136	425623126	2.7e-06	2.7	0.47	2.7
C->A	350	576192938	6.1e-07	0.61	0.11	4.4
A->mut	611	556925266	1.1e-06	1.1	0.19	3.9
indel+null	805	1133118204	7.1e-07	0.71	0.12	NaN
double_null	19	1133118204	1.7e-08	0.017	0.0029	NaN
Total	6457	1133118204	5.7e-06	5.7	1	3.5

+ Target Coverage for Each Individual

+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

+ Needs description.

+ 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: Tp*C->(T/G)
n2 = number of nonsilent mutations of type: (A/C/G)p*C->(T/G)
n3 = number of nonsilent mutations of type: C->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_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: 4. 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_cons	p_joint	p_cv	p	q
1	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	126650	11	9	4	0	10	0	0	1	0	0	0.025	0	0.00037	0	0
2	PRSS48	protease, serine, 48	38982	16	2	9	3	0	3	2	9	2	0	0.98	0	0.28	0	0
3	UGT2B10	UDP glucuronosyltransferase 2 family, polypeptide B10	122318	19	2	13	3	2	3	1	13	0	0	1	0	0.99	0	0
4	TMCC1	transmembrane and coiled-coil domain family 1	77000	4	4	3	0	0	0	1	0	3	0	0.096	0.00014	0.00023	6e-07	0.0027
5	CDC27	cell division cycle 27 homolog (S. cerevisiae)	97176	7	5	4	0	0	0	1	3	3	0	0.05	0.0092	0.00025	0.000033	0.12
6	UGT3A2	UDP glycosyltransferase 3 family, polypeptide A2	62290	3	3	2	0	1	0	0	0	2	0	0.0024	0.0013	0.0023	4e-05	0.12
7	MAPK1	mitogen-activated protein kinase 1	38660	3	3	1	0	3	0	0	0	0	0	0.2	0.00065	0.0046	0.000041	0.12
8	SEH1L	SEH1-like (S. cerevisiae)	50533	2	2	1	0	0	0	0	0	2	0	0.016	0.0056	0.0061	0.00038	0.85
9	PLAC4	placenta-specific 4	7160	2	2	2	0	0	0	0	0	1	1	0.07	0.2	0.00019	0.00043	0.87
10	PRB2	proline-rich protein BstNI subfamily 2	49240	6	4	5	0	0	0	0	1	5	0	0.34	0.76	0.000055	0.00046	0.87
11	PTEN	phosphatase and tensin homolog (mutated in multiple advanced cancers 1)	45935	3	3	3	0	0	0	0	0	3	0	0.82	0.39	0.00015	0.00064	1
12	NFE2L2	nuclear factor (erythroid-derived 2)-like 2	69545	7	6	6	0	4	0	0	1	2	0	0.049	0.18	0.0004	0.00076	1
13	OR10G8	olfactory receptor, family 10, subfamily G, member 8	36617	18	2	12	15	0	10	0	7	1	0	1	0.000085	0.96	0.00085	1
14	ITGAX	integrin, alpha X (complement component 3 receptor 4 subunit)	131027	8	4	6	6	2	2	0	3	1	0	0.59	0.00014	0.75	0.0011	1
15	PRG4	proteoglycan 4	166081	14	5	11	0	2	1	1	0	10	0	0.44	0.00018	0.86	0.0015	1
16	RAET1L	retinoic acid early transcript 1L	25451	5	2	4	0	1	1	0	3	0	0	0.53	0.0019	0.085	0.0016	1
17	NFYB	nuclear transcription factor Y, beta	25367	2	2	1	0	0	0	0	0	2	0	0.018	0.12	0.0016	0.0018	1
18	TREML4	triggering receptor expressed on myeloid cells-like 4	23897	5	2	4	3	0	3	0	1	1	0	0.88	0.021	0.012	0.0023	1
19	USP26	ubiquitin specific peptidase 26	107055	2	2	2	0	1	0	0	0	1	0	0.0056	0.0026	0.12	0.0029	1
20	CPNE3	copine III	64568	3	2	3	0	2	0	0	0	1	0	0.98	0.0019	0.45	0.0068	1
21	SPANXN5	SPANX family, member N5	8853	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.0069	0.0069	1
22	C20orf134	chromosome 20 open reading frame 134	15064	2	2	2	0	1	0	0	0	1	0	0.94	0.11	0.0078	0.0071	1
23	IFITM1	interferon induced transmembrane protein 1 (9-27)	15054	2	2	1	2	0	0	0	2	0	0	1	0.016	0.058	0.0072	1
24	PTH2	parathyroid hormone 2	8040	2	2	2	0	1	0	1	0	0	0	0.05	0.028	0.033	0.0073	1
25	ZNF645	zinc finger protein 645	49998	2	2	1	0	0	2	0	0	0	0	0.07	0.015	0.066	0.0077	1
26	LCE1C	late cornified envelope 1C	14077	4	2	2	9	0	4	0	0	0	0	0.98	0.0068	0.17	0.0088	1
27	FETUB	fetuin B	45815	2	2	2	0	1	0	0	1	0	0	0.029	0.0085	0.13	0.0089	1
28	XAGE5	X antigen family, member 5	13377	3	2	3	0	0	0	0	2	1	0	0.33	0.17	0.0071	0.0093	1
29	TMEM47	transmembrane protein 47	11233	1	1	1	0	0	0	0	0	1	0	NaN	NaN	0.0093	0.0093	1
30	IL13RA1	interleukin 13 receptor, alpha 1	48201	2	2	1	0	0	0	0	0	2	0	0.64	0.24	0.0053	0.0097	1
31	TCEAL2	transcription elongation factor A (SII)-like 2	26340	3	1	3	1	1	0	0	2	0	0	0.96	0.004	0.33	0.01	1
32	C8orf44	chromosome 8 open reading frame 44	17244	5	2	5	2	0	1	0	4	0	0	0.92	0.033	0.049	0.012	1
33	IFNGR2	interferon gamma receptor 2 (interferon gamma transducer 1)	37635	2	2	2	0	0	0	0	0	2	0	0.62	0.42	0.004	0.012	1
34	C11orf52	chromosome 11 open reading frame 52	14969	2	2	2	0	1	0	0	0	1	0	0.58	0.98	0.0019	0.014	1
35	MTL5	metallothionein-like 5, testis-specific (tesmin)	48655	2	2	2	0	0	0	0	0	2	0	0.18	0.25	0.0079	0.014	1

+ COSMIC analyses

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	PIK3CA	phosphoinositide-3-kinase, catalytic, alpha polypeptide	11	220	8	8580	3939	2.2e-13	9.8e-10
2	ATL2	atlastin GTPase 2	1	1	1	39	1	0.00022	0.17
3	EDA	ectodysplasin A	1	1	1	39	1	0.00022	0.17
4	KIAA1024	KIAA1024	2	1	1	39	1	0.00022	0.17
5	MAPK11	mitogen-activated protein kinase 11	1	1	1	39	1	0.00022	0.17
6	SUV39H2	suppressor of variegation 3-9 homolog 2 (Drosophila)	1	1	1	39	2	0.00022	0.17
7	ALS2	amyotrophic lateral sclerosis 2 (juvenile)	2	3	1	117	1	0.00067	0.23
8	EPHA10	EPH receptor A10	1	3	1	117	1	0.00067	0.23
9	IFITM3	interferon induced transmembrane protein 3 (1-8U)	5	3	1	117	1	0.00067	0.23
10	ITIH5L	inter-alpha (globulin) inhibitor H5-like	1	3	1	117	1	0.00067	0.23

+ Geneset Analyses

Table 5. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).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	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	19	ADCY1(1), ARHGEF1(1), F2R(1), F2RL3(2), GNA13(1), PIK3CA(11), PIK3R1(1), PPP1R12B(1), PRKCA(1), ROCK1(3)	1478575	23	13	16	1	16	3	1	2	0	1	0.011	0.00048	0.14
2	ACHPATHWAY	Nicotinic acetylcholine receptors are ligand-gated ion channels that primarily mediate neuromuscular signaling and may inhibit neuronal apoptosis via the AKT pathway.	AKT1, BAD, CHRNB1, CHRNG, FOXO3A, MUSK, PIK3CA, PIK3R1, PTK2, PTK2B, RAPSN, SRC, TERT, TNFSF6, YWHAH	13	CHRNG(1), MUSK(1), PIK3CA(11), PIK3R1(1), PTK2(1)	935251	15	11	8	1	11	0	1	2	1	0	0.053	0.0005	0.14
3	ERK5PATHWAY	Signaling between a tissue and its innervating axon stimulates retrograde transport via Trk receptors, which activate Erk5, which induces transcription of anti-apoptotic factors.	AKT1, CREB1, GRB2, HRAS, MAPK1, MAPK3, MAPK7, MEF2A, MEF2B, MEF2C, MEF2D, NTRK1, PIK3CA, PIK3R1, PLCG1, RPS6KA1, SHC1	17	MAPK1(3), MAPK7(1), MEF2C(1), PIK3CA(11), PIK3R1(1), RPS6KA1(2)	1088110	19	11	10	1	14	1	0	3	1	0	0.03	0.00078	0.14
4	GCRPATHWAY	Corticosteroids activate the glucocorticoid receptor (GR), which inhibits NF-kB and activates Annexin-1, thus inhibiting the inflammatory response.	ADRB2, AKT1, ANXA1, CALM1, CALM2, CALM3, CRN, GNAS, GNB1, GNGT1, HSPCA, NFKB1, NOS3, NPPA, NR3C1, PIK3CA, PIK3R1, RELA, SYT1	17	CALM1(1), CALM3(1), NPPA(1), PIK3CA(11), PIK3R1(1), SYT1(1)	1019231	16	11	9	0	12	1	1	2	0	0	0.018	0.0009	0.14
5	CTLA4PATHWAY	T cell activation requires interaction with an antigen-MHC-I complex on an antigen-presenting cell (APC), as well as CD28 interaction with the APC's CD80 or 86.	CD28, CD3D, CD3E, CD3G, CD3Z, CD80, CD86, CTLA4, GRB2, HLA-DRA, HLA-DRB1, ICOS, ICOSL, IL2, ITK, LCK, PIK3CA, PIK3R1, PTPN11, TRA@, TRB@	17	CD86(1), ITK(1), PIK3CA(11), PIK3R1(1), PTPN11(1)	739491	15	9	8	0	12	1	0	2	0	0	0.018	0.0016	0.17
6	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	MAPK1(3), PIK3CA(11), PIK3R1(1), PTEN(3), PTK2(1), SOS1(1)	1108069	20	11	11	0	15	0	0	2	3	0	0.0079	0.0017	0.17
7	ST_TYPE_I_INTERFERON_PATHWAY	Type I interferon is an antiviral cytokine that induces a JAK-STAT type pathway leading to ISGF3 activation and a cellular antiviral response.	IFNAR1, IFNB1, ISGF3G, JAK1, PTPRU, REG1A, STAT1, STAT2, TYK2	8	IFNAR1(2), PTPRU(1), REG1A(1), STAT1(3), TYK2(3)	723179	10	10	10	1	7	3	0	0	0	0	0.12	0.0019	0.17
8	IFNGPATHWAY	IFN gamma signaling pathway	IFNG, IFNGR1, IFNGR2, JAK1, JAK2, STAT1	6	IFNGR1(2), IFNGR2(2), JAK2(1), STAT1(3)	473117	8	7	8	1	4	1	0	0	3	0	0.48	0.0022	0.17
9	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(1), PIK3CA(11), PIK3R1(1), POLR1A(2), POLR1C(2), TP53(2)	1168503	19	14	12	2	13	0	0	4	2	0	0.13	0.0032	0.2
10	PLCPATHWAY	Phospholipase C hydrolyzes the membrane lipid PIP2 to DAG, which activates protein kinase C, and IP3, which causes calcium influx.	AKT1, PIK3CA, PIK3R1, PLCB1, PLCG1, PRKCA, PRKCB1, VAV1	7	PIK3CA(11), PIK3R1(1), PRKCA(1)	739813	13	9	6	1	11	0	0	2	0	0	0.13	0.0032	0.2

+ Methods & Data

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