Colon/Rectal Adenocarcinoma: 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: COADREAD

- Number of patients in set: 224

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:COADREAD.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 218

- Mutations seen in COSMIC: 739

- Significantly mutated genes in COSMIC territory: 31

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

- Significantly mutated genesets: 153

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

Mutation Preprocessing

- Read 140 MAFs of type "Broad"

- Read 88 MAFs of type "Baylor"

- Total number of mutations in input MAFs: 91973

- After removing 1369 invalidated mutations: 90604

- After removing 1176 noncoding mutations: 89428

- After collapsing adjacent/redundant mutations: 82148

Mutation Filtering

- Number of mutations before filtering: 82148

- After removing 784 mutations outside gene set: 81364

- After removing 343 mutations outside category set: 81021

- After removing 34 "impossible" mutations in

- gene-patient-category bins of zero coverage: 80987

Results
Breakdown of Mutations by Type

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

type | count
--- | ---
De_novo_Start_InFrame | 21
De_novo_Start_OutOfFrame | 156
Frame_Shift_Del | 1293
Frame_Shift_Ins | 808
In_Frame_Del | 166
In_Frame_Ins | 27
Missense_Mutation | 54120
Nonsense_Mutation | 5060
Nonstop_Mutation | 36
Read-through | 10
Silent | 19135
Splice_Site | 187
Translation_Start_Site | 2
Total | 81021

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 | 20389 | 369939104 | 0.000055 | 55 | 6
*Cp(A/C/T)->mut | 21037 | 3041594232 | 6.9e-06 | 6.9 | 0.75
A->mut | 12112 | 3284997724 | 3.7e-06 | 3.7 | 0.4
*CpG->(G/A) | 562 | 369939104 | 1.5e-06 | 1.5 | 0.16
indel+null | 7461 | 6696531284 | 1.1e-06 | 1.1 | 0.12
double_null | 304 | 6696531284 | 4.5e-08 | 0.045 | 0.0049
Total | 61865 | 6696531284 | 9.2e-06 | 9.2 | 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: COADREAD.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

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

- p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene

- p_ks = p-value for clustering of mutations (Kolmogorov-Smirnoff test)

- 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: 218. 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 | APC | adenomatous polyposis coli | 1924608 | 187 | 160 | 128 | 4 | 6 | 15 | 11 | 0 | 103 | 52 | <1.00e-15 | 2e-07 | 0.87 | 0.000019 | <0.00 | <0.00
2 | FBXW7 | F-box and WD repeat domain containing 7 | 578816 | 45 | 38 | 28 | 2 | 23 | 6 | 5 | 2 | 9 | 0 | <1.00e-15 | 0.000029 | 0.018 | 0.000024 | <0.00 | <0.00
3 | SMAD4 | SMAD family member 4 | 381472 | 29 | 26 | 22 | 0 | 10 | 6 | 9 | 0 | 3 | 1 | <1.00e-15 | 0.025 | 0.00048 | 0.00016 | <0.00 | <0.00
4 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 131264 | 20 | 20 | 8 | 0 | 2 | 14 | 4 | 0 | 0 | 0 | <1.00e-15 | 0.000012 | 0.097 | 0.000015 | <0.00 | <0.00
5 | FAM123B | family with sequence similarity 123B | 743964 | 27 | 25 | 24 | 2 | 1 | 3 | 4 | 0 | 19 | 0 | 2.78e-15 | 0.0013 | 0.74 | 0.0037 | 4.44e-16 | 1.50e-12
6 | TP53 | tumor protein p53 | 289720 | 122 | 120 | 69 | 2 | 48 | 22 | 12 | 2 | 38 | 0 | <1.00e-15 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.50e-12
7 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 158368 | 96 | 96 | 11 | 0 | 0 | 91 | 4 | 0 | 1 | 0 | <1.00e-15 | 2e-07 | 0.000072 | 0 | <1.00e-15 | <1.50e-12
8 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 736288 | 40 | 33 | 21 | 2 | 6 | 20 | 14 | 0 | 0 | 0 | <1.00e-15 | 0.0013 | 2e-06 | 0 | <1.00e-15 | <1.50e-12
9 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 499744 | 23 | 22 | 4 | 0 | 0 | 0 | 23 | 0 | 0 | 0 | 1.29e-12 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.50e-12
10 | GGT1 | gamma-glutamyltransferase 1 | 358400 | 3 | 3 | 1 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 0.59 | 3.8e-06 | 5.8e-06 | 0 | <1.00e-15 | <1.50e-12
11 | OSTN | osteocrin | 92736 | 3 | 3 | 2 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0.022 | 0.25 | 0.038 | 0 | <1.00e-15 | <1.50e-12
12 | MUTYH | mutY homolog (E. coli) | 383768 | 2 | 2 | 2 | 3 | 1 | 0 | 0 | 0 | 1 | 0 | 0.59 | 0.25 | 0.022 | 0 | <1.00e-15 | <1.50e-12
13 | SMAD2 | SMAD family member 2 | 323456 | 16 | 15 | 12 | 1 | 3 | 5 | 3 | 0 | 5 | 0 | 1.88e-11 | 0.0086 | 0.12 | 0.0094 | 5.40e-12 | 7.48e-09
14 | TCF7L2 | transcription factor 7-like 2 (T-cell specific, HMG-box) | 453708 | 20 | 18 | 18 | 4 | 5 | 5 | 3 | 0 | 7 | 0 | 1.12e-10 | 0.0016 | 0.069 | 0.0019 | 6.47e-12 | 8.33e-09
15 | FAT4 | FAT tumor suppressor homolog 4 (Drosophila) | 3346084 | 73 | 39 | 73 | 21 | 19 | 30 | 19 | 1 | 4 | 0 | 3.97e-08 | 0.00014 | 0.42 | 0.00039 | 3.97e-10 | 4.77e-07
16 | KIAA1804 |  | 540708 | 18 | 15 | 16 | 0 | 8 | 7 | 1 | 0 | 2 | 0 | 7.31e-07 | 0.00028 | 0.0019 | 9e-05 | 1.61e-09 | 1.82e-06
17 | ACVR1B | activin A receptor, type IB | 340816 | 15 | 14 | 15 | 0 | 4 | 7 | 2 | 0 | 2 | 0 | 7.97e-08 | 0.051 | 0.00017 | 0.00091 | 1.76e-09 | 1.86e-06
18 | LRP1B | low density lipoprotein-related protein 1B (deleted in tumors) | 3172736 | 75 | 39 | 73 | 18 | 11 | 34 | 22 | 0 | 5 | 3 | 5.95e-10 | 0.45 | 0.77 | 0.58 | 7.93e-09 | 7.94e-06
19 | WBSCR17 | Williams-Beuren syndrome chromosome region 17 | 403312 | 19 | 19 | 18 | 3 | 10 | 5 | 1 | 0 | 3 | 0 | 3.80e-09 | 0.078 | 0.62 | 0.14 | 1.18e-08 | 0.000011
20 | MAP2K4 | mitogen-activated protein kinase kinase 4 | 252000 | 11 | 11 | 10 | 1 | 3 | 4 | 2 | 0 | 2 | 0 | 2.64e-07 | 0.011 | 0.0032 | 0.0024 | 1.43e-08 | 0.000013
21 | KRTAP5-5 | keratin associated protein 5-5 | 131768 | 4 | 4 | 1 | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0.000012 | 0.00053 | 0.000047 | 0.000093 | 2.45e-08 | 0.000021
22 | PCDH9 | protocadherin 9 | 835520 | 26 | 22 | 26 | 7 | 3 | 11 | 11 | 0 | 1 | 0 | 1.47e-09 | 0.92 | 0.88 | 1 | 3.13e-08 | 0.000026
23 | TNFRSF10C | tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain | 177840 | 6 | 6 | 2 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0.000071 | 4.2e-06 | 1 | 0.000026 | 3.92e-08 | 0.000031
24 | KLHL4 | kelch-like 4 (Drosophila) | 508704 | 16 | 16 | 16 | 3 | 6 | 8 | 2 | 0 | 0 | 0 | 2.06e-08 | 0.78 | 0.52 | 0.81 | 3.14e-07 | 0.00024
25 | DMD | dystrophin (muscular dystrophy, Duchenne and Becker types) | 2608328 | 47 | 33 | 46 | 6 | 10 | 14 | 14 | 0 | 9 | 0 | 2.45e-07 | 0.042 | 0.78 | 0.091 | 4.14e-07 | 0.00030
26 | BTNL8 | butyrophilin-like 8 | 196296 | 3 | 3 | 1 | 1 | 0 | 0 | 3 | 0 | 0 | 0 | 0.020 | 3.4e-06 | 0.059 | 1.2e-06 | 4.48e-07 | 0.00031
27 | PCBP1 | poly(rC) binding protein 1 | 229712 | 6 | 6 | 3 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0.00087 | 0.0016 | 0.0013 | 0.000046 | 7.16e-07 | 0.00048
28 | LIFR | leukemia inhibitory factor receptor alpha | 754200 | 24 | 18 | 24 | 5 | 4 | 6 | 9 | 1 | 4 | 0 | 1.05e-07 | 0.52 | 0.52 | 0.6 | 1.12e-06 | 0.00072
29 | SOX9 | SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) | 268720 | 10 | 10 | 10 | 0 | 0 | 0 | 1 | 0 | 8 | 1 | 1.17e-06 | 0.04 | 0.38 | 0.061 | 1.25e-06 | 0.00078
30 | SDK1 | sidekick homolog 1, cell adhesion molecule (chicken) | 1435964 | 30 | 27 | 28 | 9 | 19 | 7 | 3 | 0 | 1 | 0 | 0.000028 | 0.0019 | 0.24 | 0.0036 | 1.73e-06 | 0.0010
31 | ARID1A | AT rich interactive domain 1A (SWI-like) | 1311268 | 22 | 21 | 20 | 3 | 2 | 5 | 1 | 1 | 13 | 0 | 1.07e-06 | 0.093 | 0.091 | 0.11 | 1.93e-06 | 0.0011
32 | ACOT4 | acyl-CoA thioesterase 4 | 239748 | 3 | 3 | 2 | 1 | 0 | 0 | 0 | 0 | 2 | 1 | 0.043 | 4e-07 | 0.019 | 3e-06 | 2.17e-06 | 0.0012
33 | NRXN1 | neurexin 1 | 1042896 | 24 | 20 | 24 | 11 | 10 | 7 | 4 | 1 | 2 | 0 | 0.000012 | 0.016 | 0.13 | 0.015 | 2.85e-06 | 0.0016
34 | CNTN6 | contactin 6 | 711200 | 22 | 17 | 22 | 3 | 5 | 13 | 2 | 0 | 2 | 0 | 2.35e-07 | 0.82 | 0.96 | 0.96 | 3.66e-06 | 0.0019
35 | CDH2 | cadherin 2, type 1, N-cadherin (neuronal) | 609504 | 22 | 16 | 21 | 0 | 3 | 15 | 3 | 1 | 0 | 0 | 3.80e-06 | 0.035 | 0.42 | 0.06 | 3.71e-06 | 0.0019

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: 31. Number of genes displayed: 10

rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 96 | 51 | 95 | 11424 | 1013913 | 0 | 0
2 | ERBB3 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | 14 | 6 | 6 | 1344 | 6 | 0 | 0
3 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 20 | 28 | 18 | 6272 | 17998 | 0 | 0
4 | FBXW7 | F-box and WD repeat domain containing 7 | 45 | 91 | 31 | 20384 | 1228 | 0 | 0
5 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 23 | 88 | 20 | 19712 | 210160 | 0 | 0
6 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 40 | 184 | 34 | 41216 | 13256 | 0 | 0
7 | APC | adenomatous polyposis coli | 187 | 838 | 137 | 187712 | 2553 | 0 | 0
8 | TP53 | tumor protein p53 | 122 | 823 | 122 | 184352 | 45406 | 0 | 0
9 | SMAD4 | SMAD family member 4 | 29 | 159 | 19 | 35616 | 90 | 0 | 0
10 | KRTAP5-5 | keratin associated protein 5-5 | 4 | 1 | 4 | 224 | 4 | 7.4e-13 | 3.3e-10

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: 153. 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 | HSA04310_WNT_SIGNALING_PATHWAY | Genes involved in Wnt signaling pathway | APC, APC2, AXIN1, AXIN2, BTRC, CACYBP, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CCND1, CCND2, CCND3, CER1, CHD8, CHP, CREBBP, CSNK1A1, CSNK1A1L, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, CTBP1, CTBP2, CTNNB1, CTNNBIP1, CUL1, CXXC4, DAAM1, DAAM2, DKK1, DKK2, DKK4, DVL1, DVL2, DVL3, EP300, FBXW11, FOSL1, FRAT1, FRAT2, FZD1, FZD10, FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LEF1, LOC652788, LRP5, LRP6, MAP3K7, MAPK10, MAPK8, MAPK9, MMP7, MYC, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NKD1, NKD2, NLK, PLCB1, PLCB2, PLCB3, PLCB4, PORCN, PPARD, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRICKLE1, PRICKLE2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PSEN1, RAC1, RAC2, RAC3, RBX1, RHOA, ROCK1, ROCK2, RUVBL1, SENP2, SFRP1, SFRP2, SFRP4, SFRP5, SIAH1, SKP1, SMAD2, SMAD3, SMAD4, SOX17, TBL1X, TBL1XR1, TBL1Y, TCF7, TCF7L1, TCF7L2, TP53, VANGL1, VANGL2, WIF1, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B | 144 | APC(187), APC2(1), AXIN1(2), AXIN2(9), BTRC(5), CACYBP(2), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CCND2(1), CCND3(1), CER1(3), CHD8(6), CREBBP(25), CSNK1A1(2), CSNK1A1L(5), CSNK2A1(4), CSNK2A2(2), CSNK2B(2), CTBP1(1), CTBP2(2), CTNNB1(12), CTNNBIP1(1), CUL1(8), CXXC4(1), DAAM1(2), DAAM2(9), DKK1(5), DKK2(6), DKK4(7), DVL2(9), DVL3(4), EP300(15), FBXW11(8), FZD1(1), FZD10(6), FZD2(2), FZD3(13), FZD4(2), FZD6(6), FZD7(3), FZD8(1), GSK3B(8), LEF1(4), LRP5(5), LRP6(17), MAP3K7(4), MAPK10(8), MAPK8(7), MAPK9(5), MMP7(5), NFAT5(5), NFATC1(2), NFATC2(5), NFATC3(5), NFATC4(5), NKD1(3), NKD2(1), NLK(1), PLCB1(8), PLCB2(3), PLCB3(4), PLCB4(10), PORCN(2), PPARD(2), PPP2CA(1), PPP2CB(2), PPP2R1A(4), PPP2R1B(2), PPP2R2A(1), PPP2R2B(3), PPP2R2C(4), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PRICKLE1(11), PRICKLE2(6), PRKACA(1), PRKACB(1), PRKACG(3), PRKCA(4), PRKCG(10), PRKX(2), PSEN1(3), RBX1(1), RHOA(5), ROCK1(15), ROCK2(6), RUVBL1(8), SENP2(3), SFRP1(3), SFRP2(3), SFRP4(4), SFRP5(1), SIAH1(1), SKP1(1), SMAD2(16), SMAD3(9), SMAD4(29), SOX17(2), TBL1X(6), TBL1XR1(6), TBL1Y(1), TCF7(6), TCF7L1(3), TCF7L2(20), TP53(122), VANGL1(2), VANGL2(5), WIF1(2), WNT1(1), WNT10B(4), WNT11(3), WNT16(2), WNT2(1), WNT2B(3), WNT3(4), WNT3A(1), WNT4(1), WNT5A(3), WNT6(1), WNT7A(2), WNT7B(2), WNT8A(2), WNT9A(2), WNT9B(2) | 54356112 | 894 | 218 | 758 | 155 | 275 | 204 | 133 | 8 | 221 | 53 | <1.00e-15 | <1.40e-14
2 | 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 | 203 | ABI2(1), ACTN1(5), ACTN2(8), ACTN3(3), ACTN4(3), APC(187), APC2(1), ARAF(3), ARHGEF1(5), ARHGEF12(9), ARHGEF4(4), ARHGEF6(10), ARHGEF7(8), ARPC1A(5), ARPC1B(2), ARPC2(2), ARPC5(1), ARPC5L(2), BAIAP2(1), BDKRB2(3), BRAF(23), CD14(1), CDC42(1), CFL1(1), CHRM1(3), CHRM2(11), CHRM3(4), CHRM4(1), CHRM5(2), CRKL(2), CSK(3), CYFIP1(6), CYFIP2(5), DIAPH1(1), DIAPH2(12), DIAPH3(5), DOCK1(7), EGF(3), EGFR(11), EZR(2), F2(3), FGD1(8), FGD3(2), FGF1(2), FGF11(3), FGF12(3), FGF13(3), FGF14(5), FGF17(1), FGF19(1), FGF20(2), FGF21(1), FGF23(1), FGF3(1), FGF5(4), FGF6(3), FGF7(1), FGF8(1), FGF9(1), FGFR1(4), FGFR2(6), FGFR3(2), FGFR4(2), FN1(21), GIT1(3), GNA12(2), GNA13(2), GRLF1(12), IQGAP1(13), IQGAP2(12), IQGAP3(11), ITGA1(3), ITGA10(7), ITGA11(4), ITGA2(6), ITGA2B(4), ITGA3(4), ITGA4(8), ITGA5(7), ITGA6(4), ITGA7(6), ITGA8(8), ITGA9(6), ITGAD(8), ITGAE(7), ITGAL(8), ITGAM(8), ITGAV(5), ITGAX(6), ITGB1(6), ITGB2(5), ITGB3(9), ITGB4(3), ITGB5(6), ITGB6(6), ITGB7(4), ITGB8(5), KRAS(96), LIMK1(5), LIMK2(5), MAP2K1(4), MAP2K2(1), MAPK1(2), MAPK3(3), MOS(3), MRAS(1), MSN(6), MYH10(10), MYH14(12), MYH9(12), MYL2(1), MYL7(1), MYL9(2), MYLK(14), MYLK2(3), NCKAP1(9), NCKAP1L(11), NRAS(20), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PDGFA(1), PDGFRA(17), PDGFRB(6), PFN2(1), PFN4(1), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PIP4K2A(2), PIP4K2B(2), PIP4K2C(3), PIP5K1A(3), PIP5K1B(2), PIP5K1C(4), PPP1CB(2), PPP1CC(2), PPP1R12A(3), PPP1R12B(9), PTK2(5), RAF1(6), RDX(3), RHOA(5), ROCK1(15), ROCK2(6), RRAS2(2), SCIN(3), SLC9A1(4), SOS1(7), SOS2(11), SSH1(6), SSH2(4), SSH3(1), TIAM1(17), TIAM2(16), TMSL3(1), VAV1(13), VAV2(4), VAV3(12), VCL(2), WAS(1), WASF1(3), WASF2(2), WASL(7) | 94731820 | 1187 | 216 | 982 | 278 | 334 | 392 | 203 | 8 | 194 | 56 | <1.00e-15 | <1.40e-14
3 | HSA04010_MAPK_SIGNALING_PATHWAY | Genes involved in MAPK signaling pathway | ACVR1B, ACVR1C, AKT1, AKT2, AKT3, ARRB1, ARRB2, ATF2, ATF4, BDNF, BRAF, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACNB2, CACNB3, CACNB4, CACNG1, CACNG2, CACNG3, CACNG4, CACNG5, CACNG6, CACNG7, CACNG8, CASP3, CD14, CDC25B, CDC42, CHP, CHUK, CRK, CRKL, DAXX, DDIT3, DUSP1, DUSP10, DUSP14, DUSP16, DUSP2, DUSP3, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, ECSIT, EGF, EGFR, ELK1, ELK4, EVI1, FAS, FASLG, 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, FLNA, FLNB, FLNC, FOS, GADD45A, GADD45B, GADD45G, GNA12, GNG12, GRB2, HRAS, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1R2, JUN, JUND, KRAS, LOC653852, MAP2K1, MAP2K1IP1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPT, MAX, MEF2C, MKNK1, MKNK2, MOS, MRAS, MYC, NF1, NFATC2, NFATC4, NFKB1, NFKB2, NGFB, NLK, NR4A1, NRAS, NTF3, NTF5, NTRK1, NTRK2, PAK1, PAK2, PDGFA, PDGFB, PDGFRA, PDGFRB, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PPM1A, PPM1B, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PPP5C, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTPN5, PTPN7, PTPRR, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF2, RASA1, RASA2, RASGRF1, RASGRF2, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KA6, RRAS, RRAS2, SOS1, SOS2, SRF, STK3, STK4, STMN1, TAOK1, TAOK2, TAOK3, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF1A, TP53, TRAF2, TRAF6, ZAK | 247 | ACVR1B(15), ACVR1C(3), AKT1(2), AKT2(6), AKT3(1), ARRB1(1), ATF2(1), ATF4(1), BDNF(1), BRAF(23), CACNA1A(17), CACNA1B(11), CACNA1C(12), CACNA1D(8), CACNA1E(21), CACNA1F(14), CACNA1G(10), CACNA1H(2), CACNA1I(5), CACNA1S(14), CACNA2D1(11), CACNA2D2(1), CACNA2D3(6), CACNA2D4(3), CACNB1(1), CACNB2(6), CACNB3(2), CACNB4(2), CACNG1(2), CACNG2(3), CACNG3(8), CACNG4(2), CACNG5(5), CACNG6(1), CACNG7(6), CACNG8(1), CASP3(2), CD14(1), CDC25B(5), CDC42(1), CHUK(6), CRKL(2), DAXX(1), DUSP1(2), DUSP10(5), DUSP16(5), DUSP3(1), DUSP4(1), DUSP5(2), DUSP6(5), DUSP7(2), DUSP9(1), ECSIT(3), EGF(3), EGFR(11), ELK4(2), FAS(2), FASLG(1), FGF1(2), FGF11(3), FGF12(3), FGF13(3), FGF14(5), FGF17(1), FGF19(1), FGF20(2), FGF21(1), FGF23(1), FGF3(1), FGF5(4), FGF6(3), FGF7(1), FGF8(1), FGF9(1), FGFR1(4), FGFR2(6), FGFR3(2), FGFR4(2), FLNA(3), FLNB(16), FLNC(13), FOS(1), GNA12(2), GRB2(3), IKBKB(4), IL1A(1), IL1B(1), IL1R1(4), IL1R2(7), KRAS(96), MAP2K1(4), MAP2K2(1), MAP2K3(6), MAP2K4(11), MAP2K5(4), MAP2K6(3), MAP3K1(8), MAP3K10(3), MAP3K12(6), MAP3K13(9), MAP3K14(3), MAP3K2(3), MAP3K3(3), MAP3K4(18), MAP3K5(6), MAP3K6(6), MAP3K7(4), MAP3K8(2), MAP4K1(3), MAP4K2(1), MAP4K3(4), MAP4K4(8), MAPK1(2), MAPK10(8), MAPK12(2), MAPK13(1), MAPK14(3), MAPK3(3), MAPK7(3), MAPK8(7), MAPK8IP1(2), MAPK8IP3(2), MAPK9(5), MAPKAPK2(3), MAPKAPK3(1), MAPKAPK5(1), MAPT(5), MAX(1), MEF2C(9), MKNK1(1), MKNK2(3), MOS(3), MRAS(1), NF1(9), NFATC2(5), NFATC4(5), NFKB1(6), NFKB2(4), NLK(1), NR4A1(2), NRAS(20), NTF3(1), NTRK1(6), NTRK2(4), PAK1(5), PAK2(3), PDGFA(1), PDGFRA(17), PDGFRB(6), PLA2G1B(1), PLA2G2F(1), PLA2G4A(8), PLA2G6(4), PPM1A(7), PPM1B(2), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PPP5C(3), PRKACA(1), PRKACB(1), PRKACG(3), PRKCA(4), PRKCG(10), PRKX(2), PTPN5(1), PTPN7(2), PTPRR(5), RAF1(6), RAP1A(2), RAP1B(2), RAPGEF2(13), RASA1(9), RASA2(3), RASGRF1(12), RASGRF2(9), RASGRP1(5), RASGRP2(7), RASGRP3(7), RASGRP4(2), RPS6KA1(1), RPS6KA2(10), RPS6KA3(5), RPS6KA5(6), RPS6KA6(7), RRAS2(2), SOS1(7), SOS2(11), SRF(3), STK3(3), STK4(3), STMN1(2), TAOK1(5), TAOK2(3), TAOK3(4), TGFB1(1), TGFB2(9), TGFBR1(9), TGFBR2(7), TNFRSF1A(1), TP53(122), TRAF2(1), TRAF6(4), ZAK(6) | 98648272 | 1145 | 213 | 961 | 310 | 405 | 372 | 215 | 10 | 137 | 6 | <1.00e-15 | <1.40e-14
4 | ST_ADRENERGIC | Adrenergic receptors respond to epinephrine and norepinephrine signaling. | AKT1, APC, AR, ASAH1, BF, BRAF, CAMP, CCL13, CCL15, CCL16, DAG1, EGFR, GAS, GNA11, GNA15, GNAI1, GNAQ, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, MAPK10, MAPK14, PHKA2, PIK3CA, PIK3CD, PIK3R1, PITX2, PTX1, PTX3, RAF1, SRC | 34 | AKT1(2), APC(187), AR(6), ASAH1(3), BRAF(23), CCL13(1), CCL15(1), DAG1(5), EGFR(11), GNA11(1), GNA15(3), GNAI1(4), GNAQ(4), ITPKB(4), ITPR1(19), ITPR2(18), ITPR3(12), KCNJ3(6), KCNJ5(4), KCNJ9(3), MAPK1(2), MAPK10(8), MAPK14(3), PHKA2(6), PIK3CA(40), PIK3CD(3), PIK3R1(10), PITX2(2), PTX3(2), RAF1(6), SRC(3) | 18222276 | 402 | 191 | 303 | 61 | 77 | 74 | 76 | 0 | 120 | 55 | <1.00e-15 | <1.40e-14
5 | WNT_SIGNALING | Wnt signaling genes | APC, ARHA, AXIN1, C2orf31, CCND1, CCND2, CCND3, CSNK1E, CSNK1E, LOC400927, CTNNB1, DIPA, DVL1, DVL2, DVL3, FBXW2, FOSL1, FRAT1, FZD1, FZD10, FZD2, FZD3, FZD5, FZD6, FZD7, FZD8, FZD9, GSK3B, JUN, LDLR, MAPK10, MAPK9, MYC, PAFAH1B1, PLAU, PPP2R5C, PPP2R5E, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCM, PRKCQ, PRKCZ, PRKD1, RAC1, RHOA, SFRP4, TCF7, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B | 58 | APC(187), AXIN1(2), CCND2(1), CCND3(1), CTNNB1(12), DVL2(9), DVL3(4), FBXW2(3), FZD1(1), FZD10(6), FZD2(2), FZD3(13), FZD6(6), FZD7(3), FZD8(1), GSK3B(8), LDLR(5), MAPK10(8), MAPK9(5), PAFAH1B1(3), PLAU(3), PPP2R5C(3), PPP2R5E(2), PRKCA(4), PRKCD(3), PRKCE(6), PRKCG(10), PRKCH(3), PRKCI(4), PRKCQ(5), PRKD1(15), RHOA(5), SFRP4(4), TCF7(6), WNT1(1), WNT10B(4), WNT11(3), WNT16(2), WNT2(1), WNT2B(3), WNT3(4), WNT4(1), WNT5A(3), WNT6(1), WNT7A(2), WNT7B(2) | 19830148 | 380 | 187 | 317 | 61 | 83 | 73 | 42 | 2 | 128 | 52 | <1.00e-15 | <1.40e-14
6 | ALKPATHWAY | Activin receptor-like kinase 3 (ALK3) is required during gestation for cardiac muscle development. | ACVR1, APC, ATF2, AXIN1, BMP10, BMP2, BMP4, BMP5, BMP7, BMPR1A, BMPR2, CHRD, CTNNB1, DVL1, FZD1, GATA4, GSK3B, MADH1, MADH4, MADH5, MADH6, MAP3K7, MEF2C, MYL2, NKX2-5, NOG, NPPA, NPPB, RFC1, TCF1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, WNT1 | 32 | ACVR1(4), APC(187), ATF2(1), AXIN1(2), BMP10(3), BMP2(1), BMP4(2), BMP5(5), BMP7(6), BMPR1A(4), BMPR2(10), CHRD(5), CTNNB1(12), FZD1(1), GATA4(1), GSK3B(8), MAP3K7(4), MEF2C(9), MYL2(1), NKX2-5(1), NPPA(1), NPPB(1), RFC1(14), TGFB1(1), TGFB2(9), TGFBR1(9), TGFBR2(7), TGFBR3(8), WNT1(1) | 12081204 | 318 | 185 | 257 | 34 | 50 | 54 | 35 | 1 | 126 | 52 | <1.00e-15 | <1.40e-14
7 | GSK3PATHWAY | Bacterial lipopolysaccharide activates AKT to promote the survival and activation of macrophages and inhibits Gsk3-beta to promote beta-catenin accumulation in the nucleus. | AKT1, APC, AXIN1, CCND1, CD14, CTNNB1, DVL1, FZD1, GJA1, GNAI1, GSK3B, IRAK1, LBP, LEF1, LY96, MYD88, NFKB1, PDPK1, PIK3CA, PIK3R1, PPP2CA, PRKR, RELA, TIRAP, TLR4, TOLLIP, WNT1 | 26 | AKT1(2), APC(187), AXIN1(2), CD14(1), CTNNB1(12), FZD1(1), GJA1(7), GNAI1(4), GSK3B(8), IRAK1(1), LBP(1), LEF1(4), LY96(2), MYD88(2), NFKB1(6), PDPK1(1), PIK3CA(40), PIK3R1(10), PPP2CA(1), RELA(2), TIRAP(1), TLR4(10), TOLLIP(1), WNT1(1) | 10111476 | 307 | 183 | 228 | 28 | 44 | 50 | 43 | 1 | 115 | 54 | <1.00e-15 | <1.40e-14
8 | HSA04110_CELL_CYCLE | Genes involved in cell cycle | ABL1, ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, ATM, ATR, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDC14A, CDC14B, CDC16, CDC2, CDC20, CDC23, CDC25A, CDC25B, CDC25C, CDC26, CDC27, CDC45L, CDC6, CDC7, CDK2, CDK4, CDK6, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CHEK1, CHEK2, CREBBP, CUL1, DBF4, E2F1, E2F2, E2F3, EP300, ESPL1, FZR1, GADD45A, GADD45B, GADD45G, GSK3B, hCG_1982709, HDAC1, HDAC2, LOC440917, LOC728919, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PKMYT1, PLK1, PRKDC, PTTG1, PTTG2, RB1, RBL1, RBL2, RBX1, SFN, SKP1, SKP2, SMAD2, SMAD3, SMAD4, SMC1A, SMC1B, TFDP1, TGFB1, TGFB2, TGFB3, TP53, WEE1, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ | 109 | ABL1(4), ANAPC1(4), ANAPC10(2), ANAPC2(1), ANAPC4(4), ANAPC5(3), ANAPC7(4), ATM(37), ATR(17), BUB1(6), BUB1B(6), BUB3(2), CCNA1(6), CCNA2(3), CCNB1(2), CCNB2(2), CCNB3(7), CCND2(1), CCND3(1), CCNE1(3), CCNE2(2), CCNH(2), CDC14A(4), CDC14B(4), CDC16(4), CDC20(3), CDC23(6), CDC25A(2), CDC25B(5), CDC25C(4), CDC27(13), CDC6(1), CDC7(3), CDK2(2), CDK4(3), CDK6(1), CDK7(1), CDKN1A(1), CDKN1B(3), CDKN2A(1), CDKN2C(1), CHEK1(1), CHEK2(1), CREBBP(25), CUL1(8), DBF4(5), E2F2(1), E2F3(2), EP300(15), ESPL1(8), GSK3B(8), HDAC1(2), HDAC2(2), MAD1L1(2), MAD2L1(1), MAD2L2(1), MCM3(3), MCM4(4), MCM5(6), MCM6(4), MCM7(3), MDM2(4), ORC1L(1), ORC3L(1), ORC4L(1), ORC5L(1), PCNA(3), PKMYT1(1), PLK1(8), PRKDC(18), PTTG1(1), RB1(7), RBL1(5), RBL2(8), RBX1(1), SKP1(1), SKP2(1), SMAD2(16), SMAD3(9), SMAD4(29), SMC1A(10), SMC1B(6), TFDP1(4), TGFB1(1), TGFB2(9), TP53(122), WEE1(3), YWHAB(2), YWHAE(3), YWHAH(1), YWHAQ(1) | 46359792 | 561 | 182 | 490 | 105 | 172 | 159 | 112 | 9 | 105 | 4 | <1.00e-15 | <1.40e-14
9 | HSA04210_APOPTOSIS | Genes involved in apoptosis | AIFM1, AKT1, AKT2, AKT3, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CAPN1, CAPN2, CASP10, CASP3, CASP6, CASP7, CASP8, CASP9, CFLAR, CHP, CHUK, CSF2RB, CYCS, DFFA, DFFB, ENDOG, FADD, FAS, FASLG, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1RAP, IL3, IL3RA, IRAK1, IRAK2, IRAK3, IRAK4, MAP3K14, MYD88, NFKB1, NFKB2, NFKBIA, NGFB, NTRK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, RELA, RIPK1, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF1A, TNFSF10, TP53, TRADD, TRAF2 | 80 | AIFM1(2), AKT1(2), AKT2(6), AKT3(1), APAF1(8), ATM(37), BAD(1), BAX(1), BCL2(1), BCL2L1(1), BID(1), BIRC2(4), BIRC3(7), CAPN1(2), CAPN2(6), CASP10(2), CASP3(2), CASP6(2), CASP7(1), CASP8(11), CASP9(2), CFLAR(3), CHUK(6), CSF2RB(7), DFFA(3), DFFB(2), FAS(2), FASLG(1), IKBKB(4), IL1A(1), IL1B(1), IL1R1(4), IL1RAP(1), IL3(3), IRAK1(1), IRAK2(8), IRAK3(3), IRAK4(4), MAP3K14(3), MYD88(2), NFKB1(6), NFKB2(4), NTRK1(6), PIK3CA(40), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PRKACA(1), PRKACB(1), PRKACG(3), PRKAR1A(5), PRKAR1B(1), PRKAR2B(3), RELA(2), RIPK1(2), TNFRSF10A(3), TNFRSF10B(6), TNFRSF10C(6), TNFRSF10D(1), TNFRSF1A(1), TNFSF10(1), TP53(122), TRADD(1), TRAF2(1) | 28091296 | 424 | 181 | 343 | 69 | 136 | 131 | 73 | 2 | 78 | 4 | <1.00e-15 | <1.40e-14
10 | PITX2PATHWAY | The bicoid-related transcription factor Pitx2 is activated by Wnt binding to the Frizzled receptor and induces tissue-specific cell proliferation. | APC, AXIN1, CREBBP, CTNNB1, DVL1, EP300, FZD1, GSK3B, HDAC1, HTATIP, LDB1, LEF1, PITX2, PPARBP, TRRAP, WNT1 | 14 | APC(187), AXIN1(2), CREBBP(25), CTNNB1(12), EP300(15), FZD1(1), GSK3B(8), HDAC1(2), LDB1(5), LEF1(4), PITX2(2), TRRAP(21), WNT1(1) | 10969528 | 285 | 180 | 225 | 29 | 46 | 36 | 32 | 2 | 117 | 52 | <1.00e-15 | <1.40e-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 | n6 | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | 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@ | 16 | CD28(2), CD3D(1), CD3G(2), CD80(1), CTLA4(2), GRB2(3), HLA-DRA(5), HLA-DRB1(2), ICOS(1), IL2(4), ITK(11), LCK(3), PIK3R1(10), PTPN11(5) | 3496216 | 52 | 30 | 50 | 10 | 15 | 19 | 7 | 0 | 7 | 4 | 0.0004 | 0.25
2 | CREMPATHWAY | The transcription factor CREM activates a post-meiotic transcriptional cascade culminating in spermatogenesis. | ADCY1, CREM, FHL5, FSHB, FSHR, GNAS, XPO1 | 7 | ADCY1(8), CREM(4), FHL5(4), FSHB(2), FSHR(7), GNAS(6), XPO1(2) | 3165356 | 33 | 29 | 33 | 12 | 13 | 9 | 7 | 1 | 3 | 0 | 0.00095 | 0.29
3 | ALTERNATIVEPATHWAY | The alternative complement pathway is an antibody-independent mechanism of immune activation that results in cell lysis via the membrane attack complex. | BF, C3, C5, C6, C7, C8A, C9, DF, PFC | 6 | C3(11), C5(13), C6(13), C7(5), C8A(6), C9(5) | 4331412 | 53 | 30 | 53 | 14 | 16 | 19 | 10 | 0 | 7 | 1 | 0.0046 | 0.52
4 | 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 | 6 | AKT1(2), PIK3R1(10), PLCB1(8), PLCG1(4), PRKCA(4), VAV1(13) | 3613868 | 41 | 31 | 40 | 12 | 16 | 9 | 7 | 1 | 6 | 2 | 0.006 | 0.52
5 | EOSINOPHILSPATHWAY | Recruitment of eosinophils in the inflammatory response observed in asthma occurs via the chemoattractant eotaxin binding to the CCR3 receptor. | CCL11, CCL5, CCR3, CSF2, HLA-DRA, HLA-DRB1, IL3, IL5 | 8 | CCR3(4), HLA-DRA(5), HLA-DRB1(2), IL3(3) | 943012 | 14 | 12 | 13 | 4 | 7 | 5 | 0 | 0 | 0 | 2 | 0.006 | 0.52
6 | 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 | 78 | ABL1(4), ABL2(7), AKT1(2), AKT2(6), AKT3(1), ARAF(3), BAD(1), BTC(2), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CBL(5), CBLB(8), CDKN1A(1), CDKN1B(3), CRKL(2), EGF(3), EGFR(11), ERBB2(10), EREG(1), GAB1(6), GRB2(3), GSK3B(8), HBEGF(1), MAP2K1(4), MAP2K2(1), MAPK1(2), MAPK10(8), MAPK3(3), MAPK8(7), MAPK9(5), NCK1(1), NRG1(15), NRG2(6), NRG3(7), NRG4(1), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R1(10), PIK3R2(1), PIK3R3(4), PIK3R5(1), PLCG1(4), PLCG2(13), PRKCA(4), PRKCG(10), PTK2(5), RAF1(6), RPS6KB1(3), RPS6KB2(2), SHC1(3), SHC2(1), SHC3(1), SHC4(5), SOS1(7), SOS2(11), SRC(3), STAT5B(3) | 31193464 | 293 | 101 | 284 | 87 | 100 | 82 | 60 | 3 | 46 | 2 | 0.0072 | 0.52
7 | GABAPATHWAY | Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter whose receptor is regulated by Plic-1, gephyrin, and GABARAP, which promote receptor clustering. | DNM1, GABARAP, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPHN, NSF, SRC, UBQLN1 | 11 | DNM1(11), GABRA1(4), GABRA2(9), GABRA3(5), GABRA4(8), GABRA6(5), GPHN(12), NSF(1), SRC(3), UBQLN1(2) | 3769808 | 60 | 32 | 57 | 20 | 16 | 26 | 11 | 0 | 7 | 0 | 0.0092 | 0.52
8 | 1_AND_2_METHYLNAPHTHALENE_DEGRADATION |  | ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1 | 7 | ADH1A(1), ADH1B(3), ADH1C(4), ADH4(2), ADH6(6), ADH7(2), ADHFE1(6) | 1888992 | 24 | 19 | 24 | 9 | 3 | 9 | 11 | 0 | 1 | 0 | 0.01 | 0.52
9 | REELINPATHWAY | Reelin is secreted by neurons and recognized by receptors including cadherin related neuronal receptors, which promote phosphorylation of Dab1. | CDK5, CDK5R1, DAB1, FYN, LRP8, RELN, VLDLR | 7 | CDK5R1(1), DAB1(7), FYN(5), LRP8(4), RELN(33), VLDLR(5) | 4690340 | 55 | 33 | 53 | 19 | 14 | 21 | 12 | 1 | 7 | 0 | 0.011 | 0.52
10 | GPCRDB_CLASS_C_METABOTROPIC_GLUTAMATE_PHEROMONE |  | CASR, GABBR1, GPCR5A, GPR51, GPRC5A, GPRC5B, GPRC5C, GPRC5D, GRM1, GRM2, GRM3, GRM4, GRM5, GRM7, GRM8 | 13 | CASR(7), GABBR1(6), GPRC5A(2), GPRC5B(2), GPRC5C(2), GPRC5D(1), GRM1(12), GRM2(4), GRM3(7), GRM4(7), GRM5(11), GRM7(12), GRM8(9) | 6796908 | 82 | 48 | 80 | 47 | 35 | 23 | 14 | 1 | 9 | 0 | 0.011 | 0.52

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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