Acute Myeloid Leukemia: Mutation Analysis (MutSig)

Maintained by Dan DiCara (Broad Institute)

Overview

Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v2.0 was used to generate the results found in this report.

Working with individual set: LAML.

Number of patients in set: 199

Input

The input for this pipeline is a set of individuals with the following files associated for each:

1. An annotated .maf file describing the mutations called for the respective individual, and their properties.

2. A .wig file that contains information about the coverage of the sample.

Summary

MAF used for this analysis: LAML.final_analysis_set.maf

Significantly mutated genes (q ≤ 0.1): 75

Mutations seen in COSMIC: 234

Significantly mutated genes in COSMIC territory: 18

Genes with clustered mutations (≤ 3 aa apart): 0

Significantly mutated genesets: 73

Significantly mutated genesets: (excluding sig. mutated genes): 0

Mutation Preprocessing

Read 199 MAFs of type "WashU"

Total number of mutations in input MAFs: 5617

After removing 98 mutations outside chr1-24: 5519

After removing 387 noncoding mutations: 5132

After collapsing adjacent/redundant mutations: 5126

Mutation Filtering

Number of mutations before filtering: 5126

After removing 640 mutations outside gene set: 4486

After removing 10 mutations outside category set: 4476

Results

Breakdown of Mutations by Type

Table 1. Get Full Table Table representing breakdown of mutations by type.

type	count
Frame_Shift_Del	102
Frame_Shift_Ins	118
In_Frame_Del	100
In_Frame_Ins	58
Missense_Mutation	2728
Nonsense_Mutation	191
Nonstop_Mutation	2
Silent	1073
Splice_Site	104
Total	4476

Breakdown of Mutation Rates by Category Type

Table 2. Get Full Table A breakdown of mutation rates per category discovered for this individual set.

category	n	N	rate	rate_per_mb	relative_rate
*CpG->T	802	275075312	2.9e-06	2.9	4.7
*Cp(A/C/T)->T	690	2493147819	2.8e-07	0.28	0.45
A->G	365	2773129874	1.3e-07	0.13	0.21
transver	869	5541353005	1.6e-07	0.16	0.26
indel+null	668	5541353204	1.2e-07	0.12	0.2
double_null	9	5541353204	1.6e-09	0.0016	0.0026
Total	3403	5541353204	6.1e-07	0.61	1

Target Coverage for Each Individual

The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).

Figure 1.

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

Figure 2. Patients counts and rates file used to generate this plot: LAML.patients.counts_and_rates.txt

CoMut Plot

Figure 3. Get High-res Image The matrix in the center of the figure represents individual mutations in patient samples, color-coded by type of mutation, for the significantly mutated genes. The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on the left of the matrix shows the number of mutations in each gene. The percentages represent the fraction of tumors with at least one mutation in the specified gene. The barplot to the right of the matrix displays the q-values for the most significantly mutated genes. The purple boxplots below the matrix (only displayed if required columns are present in the provided MAF) represent the distributions of allelic fractions observed in each sample. The plot at the bottom represents the base substitution distribution of individual samples, using the same categories that were used to calculate significance.

Significantly Mutated Genes

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 75. 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	IDH1	isocitrate dehydrogenase 1 (NADP+), soluble	254123	20	20	2	0	18	0	0	2	0	0	<1.00e-15	2e-07	0.97	0.000011	<0.00	<0.00
2	U2AF1	U2 small nuclear RNA auxiliary factor 1	154822	10	10	3	0	0	6	0	4	0	0	<1.00e-15	0.000026	0.0093	0.000014	<0.00	<0.00
3	TET2	tet oncogene family member 2	696898	17	15	17	1	0	1	0	2	9	5	<1.00e-15	1	0.0015	0.006	<2.22e-16	<9.59e-13
4	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	140693	9	9	5	0	0	4	1	4	0	0	<1.00e-15	0.0048	0.2	0.0052	<2.22e-16	<9.59e-13
5	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	146663	19	17	16	0	1	3	2	3	9	1	<1.00e-15	0.015	0.12	0.015	<5.55e-16	<1.33e-12
6	WT1	Wilms tumor 1	166364	13	13	9	0	1	1	0	0	10	1	<1.00e-15	0.0086	1	0.019	<7.77e-16	<1.33e-12
7	TP53	tumor protein p53	260889	15	11	15	1	3	2	4	1	5	0	<1.00e-15	0.0074	0.18	0.02	<7.77e-16	<1.33e-12
8	FLT3	fms-related tyrosine kinase 3	603169	53	52	29	0	0	1	1	16	35	0	2.33e-15	2e-07	2e-07	0	<1.00e-15	<1.33e-12
9	DNMT3A	DNA (cytosine-5-)-methyltransferase 3 alpha	517997	55	50	28	0	33	2	2	4	14	0	<1.00e-15	2e-07	2e-07	0	<1.00e-15	<1.33e-12
10	NPM1	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	185269	47	47	1	0	0	0	0	0	47	0	<1.00e-15	2e-07	2e-07	0	<1.00e-15	<1.33e-12
11	IDH2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	232631	20	20	2	0	16	3	0	1	0	0	2.00e-15	2e-07	0.62	0	<1.00e-15	<1.33e-12
12	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	116614	18	18	6	0	0	9	1	8	0	0	2.00e-15	2e-07	0.13	0	<1.00e-15	<1.33e-12
13	OR5H6	olfactory receptor, family 5, subfamily H, member 6	195418	4	4	1	2	0	0	0	0	4	0	2.06e-08	4e-07	0.034	0	<1.00e-15	<1.33e-12
14	KIT	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	591229	8	7	5	0	1	0	0	5	2	0	4.87e-12	0.011	0.024	0.0079	1.23e-12	1.52e-09
15	PHF6	PHD finger protein 6	246561	6	6	6	0	0	1	0	1	4	0	7.26e-13	0.47	0.067	0.17	3.80e-12	4.38e-09
16	AP3S1	adaptor-related protein complex 3, sigma 1 subunit	106067	3	3	1	0	0	0	0	0	3	0	2.22e-07	2.8e-06	0.12	8e-07	5.40e-12	5.83e-09
17	SCRN3	secernin 3	259297	3	3	1	0	0	0	0	0	3	0	3.21e-07	8e-07	0.93	1.4e-06	1.32e-11	1.34e-08
18	MPRIP		375911	3	3	1	0	0	0	0	0	3	0	4.37e-06	2e-07	1	2e-07	2.52e-11	2.41e-08
19	CYP21A2	cytochrome P450, family 21, subfamily A, polypeptide 2	205567	4	4	1	0	0	4	0	0	0	0	1.61e-06	4e-07	1	5.8e-06	2.46e-10	2.23e-07
20	PTPN11	protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1)	362976	7	7	6	0	0	3	1	3	0	0	1.68e-10	0.075	0.13	0.077	3.36e-10	2.90e-07
21	ETV6	ets variant gene 6 (TEL oncogene)	276809	5	5	5	0	0	0	1	1	3	0	5.47e-10	0.083	0.067	0.049	6.80e-10	5.59e-07
22	NFKBIZ	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	380488	3	3	1	0	0	0	0	0	3	0	2.20e-06	0.000034	0.71	0.000034	1.82e-09	1.43e-06
23	LILRA3	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	268252	3	3	1	1	0	0	0	3	0	0	0.000032	1.2e-06	0.71	4.6e-06	3.49e-09	2.62e-06
24	C17orf97		168553	5	5	4	1	0	0	1	4	0	0	3.52e-09	0.22	0.99	0.47	3.49e-08	0.000025
25	ZNF626	zinc finger protein 626	326559	2	2	1	0	0	0	0	0	2	0	0.00027	0.0006	0.00048	2e-05	1.08e-07	0.000075
26	MUC4	mucin 4, cell surface associated	1002562	10	7	8	6	1	0	1	5	3	0	1.24e-08	0.99	0.87	1	2.39e-07	0.00016
27	SMC3	structural maintenance of chromosomes 3	746449	6	6	6	0	1	1	1	1	2	0	2.05e-08	0.79	0.29	0.83	3.22e-07	0.00021
28	ARSD	arylsulfatase D	356608	2	2	1	0	0	0	0	2	0	0	0.0066	0.00073	0.000078	3e-06	3.70e-07	0.00023
29	NOTCH2NL	Notch homolog 2 (Drosophila) N-terminal like	144673	3	3	2	0	0	0	0	0	3	0	9.67e-07	NaN	NaN	NaN	9.67e-07	0.00058
30	PRSS16	protease, serine, 16 (thymus)	290142	2	2	1	0	0	0	0	0	2	0	0.000061	0.00068	0.65	0.0012	1.29e-06	0.00074
31	CCDC144B	coiled-coil domain containing 144B	212930	2	2	1	0	0	0	0	0	2	0	0.000031	0.00091	0.33	0.0035	1.82e-06	0.0010
32	C16orf71	chromosome 16 open reading frame 71	278600	2	2	1	0	0	0	0	0	2	0	0.00090	0.00071	0.001	0.00012	1.91e-06	0.0010
33	SKA3		241785	2	2	1	0	0	0	0	0	2	0	0.00023	0.00082	0.37	0.00071	2.70e-06	0.0014
34	ACTRT2	actin-related protein T2	188851	2	2	1	0	0	0	0	0	2	0	0.00021	0.0011	0.51	0.0011	3.66e-06	0.0019
35	FAM5C	family with sequence similarity 5, member C	463471	6	5	6	0	4	1	0	1	0	0	5.57e-07	0.74	0.52	0.85	7.38e-06	0.0036

Note:

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: A->G .

n4 - number of nonsilent mutations of type: transver .

n5 - number of nonsilent mutations of type: indel+null .

null - mutation category that includes nonsense, frameshift, splice-site mutations

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 = p-value (overall)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

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: 18. Number of genes displayed: 10

rank	gene	description	n	cos	n_cos	N_cos	cos_ev	p	q
1	TP53	tumor protein p53	15	823	15	163777	3379	0	0
2	IDH1	isocitrate dehydrogenase 1 (NADP+), soluble	20	3	20	597	29840	2.4e-15	5.3e-12
3	IDH2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	20	6	20	1194	2000	4.6e-15	6.6e-12
4	NRAS	neuroblastoma RAS viral (v-ras) oncogene homolog	18	28	18	5572	13364	2.2e-14	1.7e-11
5	NPM1	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	47	29	47	5771	172819	2.2e-14	1.7e-11
6	PTPN11	protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1)	7	31	6	6169	260	2.4e-14	1.7e-11
7	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	9	51	8	10149	62973	3.9e-14	2.5e-11
8	FLT3	fms-related tyrosine kinase 3	53	114	49	22686	6227	8.7e-14	4.8e-11
9	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene)	19	175	17	34825	88	1.3e-13	5.6e-11
10	KIT	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	8	183	7	36417	3934	1.4e-13	5.6e-11

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

There were no clustered mutations discovered.

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: 73. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	HSA04060_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION	Genes involved in cytokine-cytokine receptor interaction	ACVR1, ACVR1B, ACVR2A, ACVR2B, AMH, AMHR2, BMP2, BMP7, BMPR1A, BMPR1B, BMPR2, CCL1, CCL11, CCL13, CCL14, CCL15, CCL16, CCL17, CCL18, CCL19, CCL2, CCL20, CCL21, CCL22, CCL23, CCL24, CCL25, CCL26, CCL27, CCL28, CCL3, CCL4, CCL5, CCL7, CCL8, CCR1, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CD27, CD40, CD40LG, CD70, CLCF1, CNTF, CNTFR, CRLF2, CSF1, CSF1R, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, CX3CL1, CX3CR1, CXCL1, CXCL10, CXCL11, CXCL12, CXCL13, CXCL14, CXCL16, CXCL2, CXCL3, CXCL5, CXCL6, CXCL9, CXCR3, CXCR4, CXCR6, EDA, EDA2R, EDAR, EGF, EGFR, EPO, EPOR, FAS, FASLG, FLJ78302, FLT1, FLT3, FLT3LG, FLT4, GDF5, GH1, GH2, GHR, HGF, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNE1, IFNG, IFNGR1, IFNGR2, IFNK, IFNW1, IL10, IL10RA, IL10RB, IL11, IL11RA, IL12A, IL12B, IL12RB1, IL12RB2, IL13, IL13RA1, IL15, IL15RA, IL17A, IL17B, IL17RA, IL17RB, IL18, IL18R1, IL18RAP, IL19, IL1A, IL1B, IL1R1, IL1R2, IL1RAP, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL25, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL8, IL8RA, IL8RB, IL9, IL9R, INHBA, INHBB, INHBC, INHBE, KDR, KIT, KITLG, LEP, LEPR, LIF, LIFR, LOC728045, LTA, LTB, LTBR, MET, MPL, NGFR, OSM, OSMR, PDGFB, PDGFC, PDGFRA, PDGFRB, PF4, PF4V1, PLEKHO2, PPBP, PRL, PRLR, RELT, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF11A, TNFRSF11B, TNFRSF12A, TNFRSF13B, TNFRSF13C, TNFRSF14, TNFRSF17, TNFRSF18, TNFRSF19, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF4, TNFRSF6B, TNFRSF8, TNFRSF9, TNFSF10, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, TPO, TSLP, VEGFA, VEGFB, VEGFC, XCL1, XCL2, XCR1	242	ACVR2B(1), CCL11(1), CCL16(1), CCL17(1), CCL20(1), CCL21(1), CD70(1), CLCF1(1), CSF3R(2), CXCL16(1), EGF(1), EGFR(2), FLT1(1), FLT3(53), GHR(1), IFNA16(1), IL1R1(1), IL23R(1), IL25(1), KDR(2), KIT(8), KITLG(1), MPL(1), PDGFRA(1), PDGFRB(1), PLEKHO2(1), TPO(1)	50091285	89	80	62	10	7	10	3	31	38	<1.00e-15	<3.08e-14
2	HSA04640_HEMATOPOIETIC_CELL_LINEAGE	Genes involved in hematopoietic cell lineage	ANPEP, CD14, CD19, CD1A, CD1B, CD1C, CD1D, CD1E, CD2, CD22, CD24, CD33, CD34, CD36, CD37, CD38, CD3D, CD3E, CD3G, CD4, CD44, CD5, CD55, CD59, CD7, CD8A, CD8B, CD9, CR1, CR2, CSF1, CSF1R, CSF2, CSF2RA, CSF3, CSF3R, DNTT, EPO, EPOR, FCER2, FCGR1A, FLT3, FLT3LG, GP1BA, GP1BB, GP5, GP9, GYPA, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, IL11, IL11RA, IL1A, IL1B, IL1R1, IL1R2, IL2RA, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL7, IL7R, IL9R, ITGA1, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGAM, ITGB3, KIT, KITLG, MME, MS4A1, TFRC, THPO, TNF, TPO	83	CR1(1), CSF3R(2), FLT3(53), IL1R1(1), ITGA4(1), KIT(8), KITLG(1), MS4A1(1), TPO(1)	24232827	69	66	42	3	3	3	1	24	38	<1.00e-15	<3.08e-14
3	HSA00271_METHIONINE_METABOLISM	Genes involved in methionine metabolism	AHCY, AMD1, BHMT, CBS, CTH, DNMT1, DNMT3A, DNMT3B, KIAA0828, MARS, MARS2, MAT1A, MAT2B, MTAP, MTFMT, MTR, SRM, TAT	17	CBS(1), DNMT1(2), DNMT3A(55), DNMT3B(2), MAT1A(1)	5761050	61	54	34	0	35	2	4	6	14	<1.00e-15	<3.08e-14
4	METHIONINE_METABOLISM		AHCY, BHMT, CBS, CTH, DNMT1, DNMT2, DNMT3A, DNMT3B, MARS, MARS2, MAT1A, MAT2B, MTR	12	CBS(1), DNMT1(2), DNMT3A(55), DNMT3B(2), MAT1A(1)	4890226	61	54	34	0	35	2	4	6	14	<1.00e-15	<3.08e-14
5	ERYTHPATHWAY	Erythropoietin selectively stimulates erythrocyte differentiation from CFU-GEMM cells in bone marrow.	CCL3, CSF2, CSF3, EPO, FLT3, IGF1, IL11, IL1A, IL3, IL6, IL9, KITLG, TGFB1, TGFB2, TGFB3	14	FLT3(53), KITLG(1)	2401930	54	53	30	0	0	1	1	17	35	<1.00e-15	<3.08e-14
6	HSA04530_TIGHT_JUNCTION	Genes involved in tight junction	ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK	126	CDC42(1), CGN(1), CLDN11(1), CLDN16(1), CLDN18(1), CTNNA2(1), EXOC4(1), GNAI2(1), HCLS1(1), IGSF5(1), JAM2(1), KRAS(9), LLGL2(1), MAGI1(1), MAGI2(1), MAGI3(1), MLLT4(2), MYH1(1), MYH13(2), MYH14(1), MYH15(1), MYH6(2), MYH7(2), MYL9(1), NRAS(18), PARD3(1), PPP2R1B(1), PPP2R2B(1), PPP2R3A(1), PRKCG(1), TJAP1(3), TJP1(1), TJP2(1)	55248171	64	51	47	13	12	19	6	22	5	<1.00e-15	<3.08e-14
7	HSA04540_GAP_JUNCTION	Genes involved in gap junction	ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRB1, CDC2, CSNK1D, DRD1, DRD2, EDG2, EGF, EGFR, GJA1, GJD2, GNA11, GNAI1, GNAI2, GNAI3, GNAQ, GNAS, GRB2, GRM1, GRM5, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, HRAS, HTR2A, HTR2B, HTR2C, ITPR1, ITPR2, ITPR3, KRAS, LOC643224, LOC654264, MAP2K1, MAP2K2, MAP2K5, MAP3K2, MAPK1, MAPK3, MAPK7, NPR1, NPR2, NRAS, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PLCB1, PLCB2, PLCB3, PLCB4, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKG1, PRKG2, PRKX, PRKY, RAF1, SOS1, SOS2, SRC, TJP1, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8	90	ADCY2(1), ADCY3(1), ADCY4(2), ADCY5(1), DRD2(1), EGF(1), EGFR(2), GNAI2(1), GRM5(1), GUCY1B3(2), GUCY2C(1), GUCY2D(1), ITPR1(1), ITPR3(1), KRAS(9), MAPK1(1), NRAS(18), PDGFRA(1), PDGFRB(1), PLCB3(1), PRKCG(1), PRKG2(1), SOS1(1), TJP1(1), TUBA1A(1), TUBA1B(1), TUBA3C(2), TUBB3(1), TUBB4(1), TUBB6(1), TUBB8(1)	37538564	60	51	44	10	9	24	4	21	2	<1.00e-15	<3.08e-14
8	NUCLEAR_RECEPTORS		ALK, AR, ESR1, ESR2, ESRRA, HNF4A, NPM1, NR0B1, NR1D2, NR1H2, NR1H3, NR1I2, NR1I3, NR2C2, NR2E1, NR2F1, NR2F2, NR2F6, NR3C1, NR4A1, NR4A2, NR5A1, NR5A2, PGR, PPARA, PPARD, PPARG, RARA, RARB, RARG, ROR1, RORA, RORC, RXRA, RXRB, RXRG, THRA, THRA, NR1D1, THRB, VDR	38	NPM1(47), NR1D1(1), NR1D2(1), NR2E1(2), THRA(1), THRB(1)	11707369	53	51	7	1	1	2	0	2	48	<1.00e-15	<3.08e-14
9	HSA04650_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY	Genes involved in natural killer cell mediated cytotoxicity	ARAF, BID, BRAF, CASP3, CD244, CD247, CD48, CHP, CSF2, FAS, FASLG, FCER1G, FCGR3A, FCGR3B, FYN, GRB2, GZMB, HCST, HLA-A, HLA-B, HLA-C, HLA-E, HLA-G, HRAS, ICAM1, ICAM2, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNG, IFNGR1, IFNGR2, ITGAL, ITGB2, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DS1, KIR2DS2, KIR3DL1, KIR3DL2, KLRC1, KLRC2, KLRC3, KLRD1, KLRK1, KRAS, LAT, LCK, LCP2, LOC652578, MAP2K1, MAP2K2, MAPK1, MAPK3, MICA, MICB, NCR1, NCR2, NCR3, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NRAS, PAK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRF1, PRKCA, PRKCB1, PRKCG, PTK2B, PTPN11, PTPN6, RAC1, RAC2, RAC3, RAF1, SH2D1A, SH2D1B, SH3BP2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SYK, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFSF10, TYROBP, ULBP1, ULBP2, ULBP3, VAV1, VAV2, VAV3, ZAP70	122	CASP3(1), GZMB(1), HLA-B(2), IFNA16(1), ITGB2(1), KIR3DL1(3), KLRK1(1), KRAS(9), MAPK1(1), MICB(1), NFATC4(1), NRAS(18), PIK3CB(1), PIK3R2(1), PLCG2(1), PPP3CA(1), PRKCG(1), PTK2B(1), PTPN11(7), SHC1(1), SOS1(1), SYK(1), VAV3(1), ZAP70(1)	31625279	58	48	41	9	6	23	4	24	1	<1.00e-15	<3.08e-14
10	HSA04912_GNRH_SIGNALING_PATHWAY	Genes involved in GnRH signaling pathway	ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ATF4, CACNA1C, CACNA1D, CACNA1F, CACNA1S, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CDC42, CGA, EGFR, ELK1, FSHB, GNA11, GNAQ, GNAS, GNRH1, GNRH2, GNRHR, GRB2, HBEGF, HRAS, ITPR1, ITPR2, ITPR3, JUN, KRAS, LHB, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6, MAP2K7, MAP3K1, MAP3K2, MAP3K3, MAP3K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK9, MMP14, MMP2, NRAS, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCB1, PLCB2, PLCB3, PLCB4, PLD1, PLD2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCD, PRKX, PRKY, PTK2B, RAF1, SOS1, SOS2, SRC	91	ADCY2(1), ADCY3(1), ADCY4(2), ADCY5(1), CACNA1D(1), CACNA1S(1), CDC42(1), EGFR(2), GNRHR(1), ITPR1(1), ITPR3(1), KRAS(9), MAP2K3(1), MAP3K4(4), MAPK1(1), NRAS(18), PLA2G2D(1), PLA2G3(1), PLCB3(1), PLD1(1), PTK2B(1), SOS1(1)	36254019	52	47	34	7	7	20	3	19	3	<1.00e-15	<3.08e-14

Table 6. 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	q
1	ERBB3PATHWAY	Neuregulins bind to the receptor tyrosine kinases ErbB3 and ErbB4, surface-localized receptors whose overexpression induces tumor formation.	EGF, EGFR, ERBB3, NRG1, UBE2D1	5	EGF(1), EGFR(2), ERBB3(2), UBE2D1(1)	2995149	6	6	6	1	1	1	0	3	1	0.00072	0.23
2	HSA05130_PATHOGENIC_ESCHERICHIA_COLI_INFECTION_EHEC	Genes involved in pathogenic Escherichia coli infection - EHEC	ABL1, ACTB, ACTG1, ARHGEF2, ARPC5, ARPC5L, CD14, CDC42, CDH1, CLDN1, CTNNB1, CTTN, EZR, FYN, HCLS1, ITGB1, KRT18, LOC643224, LOC654264, LY96, NCK1, NCK2, NCL, OCLN, PRKCA, RHOA, ROCK1, ROCK2, TLR4, TLR5, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8, WAS, WASL, YWHAQ, YWHAZ	51	ABL1(2), CDC42(1), EZR(1), HCLS1(1), LY96(1), TLR4(1), TUBA1A(1), TUBA1B(1), TUBA3C(2), TUBB3(1), TUBB4(1), TUBB6(1), TUBB8(1), YWHAZ(1)	15524189	16	16	16	6	4	3	2	6	1	0.0011	0.23
3	HSA05131_PATHOGENIC_ESCHERICHIA_COLI_INFECTION_EPEC	Genes involved in pathogenic Escherichia coli infection - EPEC	ABL1, ACTB, ACTG1, ARHGEF2, ARPC5, ARPC5L, CD14, CDC42, CDH1, CLDN1, CTNNB1, CTTN, EZR, FYN, HCLS1, ITGB1, KRT18, LOC643224, LOC654264, LY96, NCK1, NCK2, NCL, OCLN, PRKCA, RHOA, ROCK1, ROCK2, TLR4, TLR5, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8, WAS, WASL, YWHAQ, YWHAZ	51	ABL1(2), CDC42(1), EZR(1), HCLS1(1), LY96(1), TLR4(1), TUBA1A(1), TUBA1B(1), TUBA3C(2), TUBB3(1), TUBB4(1), TUBB6(1), TUBB8(1), YWHAZ(1)	15524189	16	16	16	6	4	3	2	6	1	0.0011	0.23
4	HSA04530_TIGHT_JUNCTION	Genes involved in tight junction	ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK	123	CDC42(1), CGN(1), CLDN11(1), CLDN16(1), CLDN18(1), CTNNA2(1), EXOC4(1), GNAI2(1), HCLS1(1), IGSF5(1), JAM2(1), LLGL2(1), MAGI1(1), MAGI2(1), MAGI3(1), MLLT4(2), MYH1(1), MYH13(2), MYH14(1), MYH15(1), MYH6(2), MYL9(1), PARD3(1), PPP2R1B(1), PPP2R2B(1), PPP2R3A(1), PRKCG(1), TJAP1(3), TJP1(1), TJP2(1)	53804824	35	29	35	13	12	6	4	10	3	0.003	0.35
5	GLUTATHIONE_METABOLISM		ANPEP, G6PD, GCLC, GCLM, GGT1, GPX1, GPX2, GPX3, GPX4, GPX5, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, PGD	27	G6PD(1), GCLM(1), GPX2(1), GSTM3(2), GSTT2(1), PGD(1)	4736200	7	7	7	1	0	4	1	2	0	0.0033	0.35
6	HSA04810_REGULATION_OF_ACTIN_CYTOSKELETON	Genes involved in regulation of actin cytoskeleton	ABI2, ACTN1, ACTN2, ACTN3, ACTN4, APC, APC2, ARAF, ARHGEF1, ARHGEF12, ARHGEF4, ARHGEF6, ARHGEF7, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ARPC5L, BAIAP2, BCAR1, BDKRB1, BDKRB2, BRAF, C3orf10, CD14, CDC42, CFL1, CFL2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CRK, CRKL, CSK, CYFIP1, CYFIP2, DIAPH1, DIAPH2, DIAPH3, DOCK1, EGF, EGFR, EZR, F2, F2R, FGD1, FGD3, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FN1, GIT1, GNA12, GNA13, GNG12, GRLF1, GSN, HRAS, INS, IQGAP1, IQGAP2, IQGAP3, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAD, ITGAE, ITGAL, ITGAM, ITGAV, ITGAX, ITGB1, ITGB2, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, KRAS, LIMK1, LIMK2, LOC200025, LOC645126, LOC653888, MAP2K1, MAP2K2, MAPK1, MAPK3, MLCK, MOS, MRAS, MRCL3, MRLC2, MSN, MYH10, MYH14, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, NCKAP1, NCKAP1L, NRAS, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDGFA, PDGFB, PDGFRA, PDGFRB, PFN1, PFN2, PFN3, PFN4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PPP1R12B, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RDX, RHOA, ROCK1, ROCK2, RRAS, RRAS2, SCIN, SLC9A1, SOS1, SOS2, SSH1, SSH2, SSH3, TIAM1, TIAM2, TMSB4X, TMSB4Y, TMSL3, VAV1, VAV2, VAV3, VCL, WAS, WASF1, WASF2, WASL	191	APC(4), ARHGEF1(1), ARHGEF6(1), BAIAP2(1), CDC42(1), DIAPH2(1), DOCK1(1), EGF(1), EGFR(2), EZR(1), FGF8(1), FN1(2), IQGAP3(3), ITGA10(1), ITGA11(1), ITGA4(1), ITGAD(2), ITGAV(1), ITGAX(1), ITGB2(1), MAPK1(1), MYH14(1), MYL9(1), MYLK(1), MYLK2(1), PDGFRA(1), PDGFRB(1), PIK3CB(1), PIK3R2(1), PIP5K1B(1), PIP5K1C(1), PPP1R12A(1), SOS1(1), SSH3(1), TIAM2(1), TMSL3(1), VAV3(1)	77184737	45	33	45	10	13	9	6	13	4	0.0034	0.35
7	CIRCADIAN_EXERCISE		ARNTL, AZIN1, BTG1, C10orf110, C1orf1, CBX3, CEBPB, CLDN5, CLOCK, CRY1, CRY2, DAZAP2, DAZAP2, LOC401029, DNAJA1, EIF4G2, ETV6, G0S2, GENX_3414, GFRA1, GSTM3, GSTP1, HERPUD1, HLA_DMA, HSPA8, IDI1, KLF9, MAP3K7IP2, MYF6, NCKAP1, NCOA4, NR1D2, OAZIN, PER1, PER2, PIGF, PPP1R3C, PPP2CB, PSMA4, PURA, SF3A3, SUMO3, TOB1, TUBB3, UCP3, UGP2, VAPA, ZFR	36	CRY1(1), DAZAP2(1), GSTM3(2), NR1D2(1), PIGF(1), PURA(1), TUBB3(1)	10039948	8	8	8	2	0	0	3	3	2	0.0059	0.52
8	HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION	Genes involved in neuroactive ligand-receptor interaction	ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2	220	ADRA1A(1), BRS3(1), C5AR1(1), CRHR2(1), CTSG(1), DRD2(1), F2RL1(1), GABBR1(1), GABRA4(1), GABRB1(1), GABRG2(1), GABRR1(1), GHR(1), GLRA1(1), GNRHR(1), GPR156(1), GPR50(1), GRID1(2), GRIK2(3), GRIK3(2), GRIK4(3), GRIK5(1), GRIN3A(1), GRM3(2), GRM5(1), GRM6(2), GRM8(2), HTR5A(1), MCHR2(1), NMUR2(3), NTSR2(1), OPRM1(1), P2RX7(1), P2RY1(1), P2RY2(2), PARD3(1), PRSS3(1), SCTR(1), SSTR4(1), THRA(1), THRB(1), VIPR1(2)	60973003	55	41	55	16	18	18	3	13	3	0.0068	0.53
9	HSA00480_GLUTATHIONE_METABOLISM	Genes involved in glutathione metabolism	ANPEP, G6PD, GCLC, GCLM, GGT1, GGTL3, GGTL4, GPX1, GPX2, GPX3, GPX4, GPX5, GPX6, GPX7, GSR, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTK1, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, OPLAH, TXNDC12	31	G6PD(1), GCLM(1), GPX2(1), GSTM3(2), GSTT2(1)	5168229	6	6	6	1	0	3	1	2	0	0.0095	0.63
10	HSA04020_CALCIUM_SIGNALING_PATHWAY	Genes involved in calcium signaling pathway	ADCY1, ADCY2, ADCY3, ADCY4, ADCY7, ADCY8, ADCY9, ADORA2A, ADORA2B, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, AGTR1, ATP2A1, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, ATP2B4, AVPR1A, AVPR1B, BDKRB1, BDKRB2, BST1, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CCKAR, CCKBR, CD38, CHP, CHRM1, CHRM2, CHRM3, CHRM5, CHRNA7, CYSLTR1, CYSLTR2, DRD1, EDNRA, EDNRB, EGFR, ERBB2, ERBB3, ERBB4, F2R, GNA11, GNA14, GNA15, GNAL, GNAQ, GNAS, GRIN1, GRIN2A, GRIN2C, GRIN2D, GRM1, GRM5, GRPR, HRH1, HRH2, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, LHCGR, LTB4R2, MLCK, MYLK, MYLK2, NOS1, NOS2A, NOS3, NTSR1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, PDE1A, PDE1B, PDE1C, PDGFRA, PDGFRB, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PLN, PPID, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTAFR, PTGER1, PTGER3, PTGFR, PTK2B, RYR1, RYR2, RYR3, SLC25A4, SLC25A5, SLC25A6, SLC8A1, SLC8A2, SLC8A3, SPHK1, SPHK2, TACR1, TACR2, TACR3, TBXA2R, TNNC1, TNNC2, TRHR, TRPC1, VDAC1, VDAC2, VDAC3	163	ADCY2(1), ADCY3(1), ADCY4(2), ADRA1A(1), ATP2A2(1), ATP2B2(1), ATP2B3(1), CACNA1B(3), CACNA1D(1), CACNA1E(3), CACNA1G(2), CACNA1I(1), CACNA1S(1), CAMK4(1), EGFR(2), ERBB3(2), GNA15(1), GRM5(1), HTR5A(1), ITPR1(1), ITPR3(1), MYLK(1), MYLK2(1), NOS1(1), P2RX7(1), PDGFRA(1), PDGFRB(1), PHKG1(1), PLCB3(1), PLCD4(1), PLCE1(4), PLCG2(1), PLCZ1(1), PPP3CA(1), PRKCG(1), PTK2B(1), RYR1(1), RYR3(4), TNNC2(1), TRPC1(1), VDAC1(1)	76549927	55	39	55	21	14	12	7	20	2	0.012	0.63

Methods & Data

Methods

In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset. [1]

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)

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