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): 340

Mutations seen in COSMIC: 739

Significantly mutated genes in COSMIC territory: 31

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

Significantly mutated genesets: 248

Significantly mutated genesets: (excluding sig. mutated genes): 66

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

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 340. 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 | 1.33e-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 | 0.098 | 0.000015 | <0.00 | <0.00
5 | FAM123B | family with sequence similarity 123B | 743964 | 27 | 25 | 24 | 2 | 1 | 3 | 4 | 0 | 19 | 0 | <1.00e-15 | 0.0018 | 0.73 | 0.0046 | <2.22e-16 | <8.01e-13
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 | <1.39e-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 | <1.39e-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 | <1.39e-12
9 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 499744 | 23 | 22 | 4 | 0 | 0 | 0 | 23 | 0 | 0 | 0 | 1.74e-13 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.39e-12
10 | ACOT4 | acyl-CoA thioesterase 4 | 239748 | 3 | 3 | 2 | 1 | 0 | 0 | 0 | 0 | 2 | 1 | 0.020 | 1.6e-06 | 0.021 | 0 | <1.00e-15 | <1.39e-12
11 | GGT1 | gamma-glutamyltransferase 1 | 358400 | 3 | 3 | 1 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 0.59 | 3.6e-06 | 3.6e-06 | 0 | <1.00e-15 | <1.39e-12
12 | OSTN | osteocrin | 92736 | 3 | 3 | 2 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0.044 | 0.25 | 0.038 | 0 | <1.00e-15 | <1.39e-12
13 | MUTYH | mutY homolog (E. coli) | 383768 | 2 | 2 | 2 | 3 | 1 | 0 | 0 | 0 | 1 | 0 | 0.54 | 0.25 | 0.022 | 0 | <1.00e-15 | <1.39e-12
14 | SMAD2 | SMAD family member 2 | 323456 | 16 | 15 | 12 | 1 | 3 | 5 | 3 | 0 | 5 | 0 | 1.60e-14 | 0.0086 | 0.12 | 0.0094 | 5.66e-15 | 7.29e-12
15 | TCF7L2 | transcription factor 7-like 2 (T-cell specific, HMG-box) | 453708 | 20 | 18 | 18 | 4 | 5 | 5 | 3 | 0 | 7 | 0 | 6.99e-14 | 0.0047 | 0.096 | 0.0062 | 1.58e-14 | 1.89e-11
16 | LRP1B | low density lipoprotein-related protein 1B (deleted in tumors) | 3172736 | 75 | 39 | 73 | 18 | 11 | 34 | 22 | 0 | 5 | 3 | <1.00e-15 | 0.45 | 0.77 | 0.58 | <2.11e-14 | <2.38e-11
17 | ACVR1B | activin A receptor, type IB | 340816 | 15 | 14 | 15 | 0 | 4 | 7 | 2 | 0 | 2 | 0 | 4.65e-09 | 0.059 | 0.00032 | 0.00062 | 7.97e-11 | 8.45e-08
18 | FAT4 | FAT tumor suppressor homolog 4 (Drosophila) | 3346084 | 73 | 39 | 73 | 21 | 19 | 30 | 19 | 1 | 4 | 0 | 6.23e-09 | 0.00018 | 0.41 | 0.00059 | 1.01e-10 | 1.01e-07
19 | DMD | dystrophin (muscular dystrophy, Duchenne and Becker types) | 2608328 | 47 | 33 | 46 | 6 | 10 | 14 | 14 | 0 | 9 | 0 | 5.83e-11 | 0.04 | 0.73 | 0.074 | 1.18e-10 | 1.07e-07
20 | ARID1A | AT rich interactive domain 1A (SWI-like) | 1311268 | 22 | 21 | 20 | 3 | 2 | 5 | 1 | 1 | 13 | 0 | 9.52e-12 | 0.52 | 0.25 | 0.46 | 1.19e-10 | 1.07e-07
21 | WBSCR17 | Williams-Beuren syndrome chromosome region 17 | 403312 | 19 | 19 | 18 | 3 | 10 | 5 | 1 | 0 | 3 | 0 | 8.46e-11 | 0.081 | 0.65 | 0.13 | 2.98e-10 | 2.55e-07
22 | ATM | ataxia telangiectasia mutated | 2109720 | 37 | 25 | 36 | 3 | 4 | 18 | 5 | 0 | 8 | 2 | 7.62e-11 | 0.27 | 0.17 | 0.18 | 3.56e-10 | 2.92e-07
23 | TTN | titin | 24865216 | 290 | 85 | 286 | 79 | 82 | 114 | 72 | 2 | 13 | 7 | 5.92e-11 | 0.5 | 0.88 | 0.55 | 8.19e-10 | 6.42e-07
24 | PCDH9 | protocadherin 9 | 835520 | 26 | 22 | 26 | 7 | 3 | 11 | 11 | 0 | 1 | 0 | 3.50e-11 | 0.92 | 0.88 | 1 | 8.77e-10 | 6.59e-07
25 | ZC3H13 | zinc finger CCCH-type containing 13 | 1066016 | 26 | 21 | 25 | 1 | 8 | 2 | 1 | 0 | 15 | 0 | 2.37e-10 | 0.5 | 0.35 | 0.61 | 3.44e-09 | 2.48e-06
26 | MAP2K4 | mitogen-activated protein kinase kinase 4 | 252000 | 11 | 11 | 10 | 1 | 3 | 4 | 2 | 0 | 2 | 0 | 1.34e-08 | 0.043 | 0.039 | 0.026 | 7.85e-09 | 5.44e-06
27 | KIAA1804 |  | 540708 | 18 | 15 | 16 | 0 | 8 | 7 | 1 | 0 | 2 | 0 | 1.95e-07 | 0.0057 | 0.011 | 0.0033 | 1.44e-08 | 9.64e-06
28 | ACVR2A | activin A receptor, type IIA | 355264 | 10 | 9 | 9 | 1 | 0 | 0 | 4 | 0 | 5 | 1 | 1.45e-07 | 0.076 | 0.0065 | 0.0065 | 2.04e-08 | 0.000013
29 | LIFR | leukemia inhibitory factor receptor alpha | 754200 | 24 | 18 | 24 | 5 | 4 | 6 | 9 | 1 | 4 | 0 | 1.85e-09 | 0.52 | 0.52 | 0.62 | 2.48e-08 | 0.000015
30 | TNFRSF10C | tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain | 177840 | 6 | 6 | 2 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0.000037 | 7e-06 | 1 | 0.000041 | 3.25e-08 | 0.000020
31 | SOX9 | SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) | 268720 | 10 | 10 | 10 | 0 | 0 | 0 | 1 | 0 | 8 | 1 | 1.06e-07 | 0.048 | 0.42 | 0.061 | 1.29e-07 | 0.000075
32 | KRTAP5-5 | keratin associated protein 5-5 | 131768 | 4 | 4 | 1 | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0.00021 | 0.00062 | 0.000023 | 0.000032 | 1.33e-07 | 0.000075
33 | ATP10A | ATPase, class V, type 10A | 971776 | 21 | 19 | 21 | 12 | 8 | 6 | 2 | 1 | 4 | 0 | 4.24e-07 | 0.018 | 0.69 | 0.031 | 2.50e-07 | 0.00014
34 | TXNDC3 | thioredoxin domain containing 3 (spermatozoa) | 409248 | 14 | 11 | 14 | 2 | 3 | 3 | 3 | 0 | 5 | 0 | 3.13e-08 | 0.47 | 0.82 | 0.73 | 4.27e-07 | 0.00023
35 | SYNE1 | spectrin repeat containing, nuclear envelope 1 | 6063232 | 100 | 47 | 98 | 30 | 23 | 42 | 27 | 0 | 7 | 1 | 5.81e-08 | 0.56 | 0.29 | 0.56 | 5.95e-07 | 0.00031

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)->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 .

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: 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: 248. 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 | <1.10e-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 | <1.10e-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 | <1.10e-14
4 | 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 | <1.10e-14
5 | 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 | <1.10e-14
6 | HSA04360_AXON_GUIDANCE | Genes involved in axon guidance | ABL1, ABLIM1, ABLIM2, ABLIM3, ARHGEF12, CDC42, CDK5, CFL1, CFL2, CHP, CXCL12, CXCR4, DCC, DPYSL2, DPYSL5, EFNA1, EFNA2, EFNA3, EFNA4, EFNA5, EFNB1, EFNB2, EFNB3, EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHB1, EPHB2, EPHB3, EPHB4, EPHB6, FES, FYN, GNAI1, GNAI2, GNAI3, GSK3B, HRAS, ITGB1, KRAS, L1CAM, LIMK1, LIMK2, LRRC4C, MAPK1, MAPK3, MET, NCK1, NCK2, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NGEF, NRAS, NRP1, NTN1, NTN2L, NTN4, NTNG1, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PLXNA1, PLXNA2, PLXNA3, PLXNB1, PLXNB2, PLXNB3, PLXNC1, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PTK2, RAC1, RAC2, RAC3, RASA1, RGS3, RHOA, RHOD, RND1, ROBO1, ROBO2, ROBO3, ROCK1, ROCK2, SEMA3A, SEMA3B, SEMA3C, SEMA3D, SEMA3E, SEMA3F, SEMA3G, SEMA4A, SEMA4B, SEMA4C, SEMA4D, SEMA4F, SEMA4G, SEMA5A, SEMA5B, SEMA6A, SEMA6B, SEMA6C, SEMA6D, SEMA7A, SLIT1, SLIT2, SLIT3, SRGAP1, SRGAP2, SRGAP3, UNC5A, UNC5B, UNC5C, UNC5D | 127 | ABL1(4), ABLIM1(6), ABLIM2(4), ABLIM3(5), ARHGEF12(9), CDC42(1), CFL1(1), CXCL12(1), CXCR4(4), DCC(16), DPYSL2(5), DPYSL5(1), EFNA3(1), EFNA4(1), EFNA5(5), EFNB1(3), EFNB2(1), EFNB3(3), EPHA1(6), EPHA2(5), EPHA3(17), EPHA4(6), EPHA5(17), EPHA6(5), EPHA7(10), EPHA8(7), EPHB1(9), EPHB2(8), EPHB3(2), EPHB4(5), EPHB6(4), FYN(5), GNAI1(4), GSK3B(8), ITGB1(6), KRAS(96), L1CAM(4), LIMK1(5), LIMK2(5), LRRC4C(8), MAPK1(2), MAPK3(3), MET(5), NCK1(1), NFAT5(5), NFATC1(2), NFATC2(5), NFATC3(5), NFATC4(5), NGEF(1), NRAS(20), NRP1(1), NTN1(5), NTN4(6), NTNG1(4), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PLXNA1(2), PLXNA2(8), PLXNA3(2), PLXNB1(5), PLXNB2(2), PLXNB3(3), PLXNC1(9), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PTK2(5), RASA1(9), RGS3(10), RHOA(5), RND1(1), ROBO1(24), ROBO2(18), ROBO3(5), ROCK1(15), ROCK2(6), SEMA3A(9), SEMA3B(1), SEMA3C(3), SEMA3D(13), SEMA3E(9), SEMA3F(1), SEMA3G(4), SEMA4A(3), SEMA4B(2), SEMA4D(13), SEMA4F(9), SEMA4G(6), SEMA5A(8), SEMA5B(11), SEMA6A(2), SEMA6B(2), SEMA6C(3), SEMA6D(9), SEMA7A(2), SLIT1(11), SLIT2(15), SLIT3(9), SRGAP1(9), SRGAP2(3), SRGAP3(4), UNC5A(2), UNC5B(6), UNC5C(12), UNC5D(9) | 66363964 | 737 | 183 | 630 | 196 | 250 | 285 | 115 | 7 | 80 | 0 | <1.00e-15 | <1.10e-14
7 | 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 | <1.10e-14
8 | 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 | <1.10e-14
9 | 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 | <1.10e-14
10 | ST_MYOCYTE_AD_PATHWAY | Cardiac myocytes have a variety of adrenergic receptors that induce subtype-specific signaling effects. | ADRB1, AKT1, APC, ASAH1, BF, CAMP, CAV3, DAG1, DLG4, EPHB2, GAS, GNAI1, GNAQ, HTATIP, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, PITX2, PLB, PTX1, PTX3, RAC1, RHO, RYR1 | 23 | ADRB1(3), AKT1(2), APC(187), ASAH1(3), CAV3(3), DAG1(5), DLG4(3), EPHB2(8), GNAI1(4), GNAQ(4), ITPR1(19), ITPR2(18), ITPR3(12), KCNJ3(6), KCNJ5(4), KCNJ9(3), MAPK1(2), PITX2(2), PTX3(2), RHO(3), RYR1(25) | 15764424 | 318 | 180 | 258 | 58 | 69 | 53 | 28 | 0 | 115 | 53 | <1.00e-15 | <1.10e-14

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 66. 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
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1 | HSA04514_CELL_ADHESION_MOLECULES | Genes involved in cell adhesion molecules (CAMs) | ALCAM, CADM1, CADM3, CD2, CD22, CD226, CD274, CD276, CD28, CD34, CD4, CD40, CD40LG, CD58, CD6, CD80, CD86, CD8A, CD8B, CD99, CDH1, CDH15, CDH2, CDH3, CDH4, CDH5, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CNTN1, CNTN2, CNTNAP1, CNTNAP2, CTLA4, ESAM, F11R, GLG1, HLA-A, HLA-A29.1, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-E, HLA-F, HLA-G, ICAM1, ICAM2, ICAM3, ICOS, ICOSLG, ITGA4, ITGA6, ITGA8, ITGA9, ITGAL, ITGAM, ITGAV, ITGB1, ITGB2, ITGB7, ITGB8, JAM2, JAM3, L1CAM, MADCAM1, MAG, MPZ, MPZL1, NCAM1, NCAM2, NEGR1, NEO1, NFASC, NLGN1, NLGN2, NLGN3, NRCAM, NRXN1, NRXN2, NRXN3, OCLN, PDCD1, PDCD1LG2, PECAM1, PTPRC, PTPRF, PTPRM, PVR, PVRL1, PVRL2, PVRL3, SDC1, SDC2, SDC3, SDC4, SELE, SELL, SELP, SELPLG, SIGLEC1, SPN, VCAM1, VCAN | 123 | ALCAM(2), CADM1(8), CADM3(8), CD2(3), CD22(10), CD226(4), CD274(4), CD28(2), CD34(1), CD4(2), CD40(1), CD40LG(6), CD58(2), CD6(3), CD80(1), CD8B(2), CDH1(5), CDH15(1), CDH3(4), CDH4(11), CDH5(2), CLDN10(4), CLDN11(1), CLDN15(1), CLDN16(5), CLDN17(5), CLDN18(2), CLDN19(1), CLDN2(1), CLDN6(2), CLDN7(2), CLDN8(5), CLDN9(1), CNTN2(7), CNTNAP1(7), CNTNAP2(12), CTLA4(2), ESAM(3), F11R(1), GLG1(4), HLA-A(3), HLA-B(3), HLA-C(2), HLA-DMA(2), HLA-DMB(1), HLA-DOA(1), HLA-DOB(1), HLA-DPA1(1), HLA-DPB1(2), HLA-DQA1(1), HLA-DQA2(3), HLA-DQB1(1), HLA-DRA(5), HLA-DRB1(2), HLA-DRB5(1), HLA-E(1), HLA-F(2), HLA-G(2), ICAM1(2), ICAM2(1), ICOS(1), ITGA4(8), ITGA6(4), ITGA8(8), ITGA9(6), ITGAL(8), ITGAM(8), ITGAV(5), ITGB1(6), ITGB2(5), ITGB7(4), ITGB8(5), JAM3(3), L1CAM(4), MAG(7), MPZL1(1), NCAM1(6), NEGR1(4), NEO1(6), NFASC(17), NLGN1(7), NLGN2(2), NLGN3(4), NRCAM(7), NRXN2(6), OCLN(1), PDCD1LG2(1), PECAM1(2), PTPRC(17), PTPRF(9), PVR(1), PVRL1(6), PVRL2(4), PVRL3(2), SDC1(1), SDC2(3), SDC3(3), SDC4(1), SELE(4), SELL(3), SELP(6), SELPLG(2), SIGLEC1(4), SPN(2), VCAM1(9), VCAN(36) | 44797856 | 444 | 107 | 434 | 172 | 153 | 150 | 79 | 3 | 55 | 4 | 1.4e-08 | 4.8e-06
2 | 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 | 239 | ACVR1(4), ACVR2B(4), AMHR2(2), BMP2(1), BMP7(6), BMPR1A(4), BMPR1B(10), BMPR2(10), CCL13(1), CCL15(1), CCL18(2), CCL22(1), CCL23(2), CCL27(3), CCL7(1), CCL8(1), CCR1(5), CCR3(4), CCR4(1), CCR5(1), CCR6(2), CCR7(3), CCR8(4), CCR9(6), CD27(3), CD40(1), CD40LG(6), CD70(5), CNTF(2), CNTFR(2), CSF1(2), CSF1R(3), CSF2RB(7), CSF3R(10), CX3CL1(1), CX3CR1(2), CXCL10(1), CXCL11(3), CXCL12(1), CXCL14(2), CXCL16(1), CXCL5(2), CXCL6(1), CXCL9(3), CXCR4(4), EDA(2), EDA2R(2), EDAR(3), EGF(3), EGFR(11), FAS(2), FASLG(1), FLT1(12), FLT3(5), FLT3LG(1), FLT4(5), GDF5(2), GH1(2), GH2(3), GHR(6), HGF(8), IFNA1(1), IFNA10(3), IFNA13(2), IFNA16(4), IFNA2(4), IFNA21(1), IFNA4(2), IFNA5(1), IFNA6(3), IFNA7(1), IFNA8(1), IFNAR1(3), IFNAR2(2), IFNB1(1), IFNG(1), IFNGR1(3), IFNGR2(2), IFNK(1), IL10(2), IL10RA(2), IL10RB(5), IL11(1), IL11RA(1), IL12A(1), IL12B(2), IL12RB1(2), IL12RB2(6), IL13(1), IL13RA1(2), IL15(1), IL15RA(1), IL17A(2), IL17RA(6), IL17RB(1), IL18RAP(4), IL19(1), IL1A(1), IL1B(1), IL1R1(4), IL1R2(7), IL1RAP(1), IL2(4), IL20(3), IL20RA(5), IL21(2), IL21R(5), IL22(2), IL22RA1(1), IL23R(3), IL24(2), IL25(1), IL26(3), IL28RA(3), IL2RA(2), IL2RB(2), IL3(3), IL4(3), IL4R(1), IL5RA(6), IL6(2), IL6R(3), IL6ST(3), IL7(2), IL7R(3), IL8(1), IL9(2), INHBB(1), INHBC(3), INHBE(1), KDR(10), KIT(8), KITLG(2), LEP(1), LEPR(9), LTB(1), LTBR(3), MET(5), MPL(2), NGFR(3), OSM(1), OSMR(6), PDGFC(3), PDGFRA(17), PDGFRB(6), PLEKHO2(5), PRL(3), PRLR(4), RELT(2), TGFB1(1), TGFB2(9), TGFBR1(9), TNFRSF10A(3), TNFRSF10B(6), TNFRSF10D(1), TNFRSF11A(3), TNFRSF11B(4), TNFRSF13B(4), TNFRSF17(2), TNFRSF19(3), TNFRSF1A(1), TNFRSF21(5), TNFRSF4(1), TNFRSF8(2), TNFRSF9(3), TNFSF10(1), TNFSF11(1), TNFSF12(2), TNFSF13B(1), TNFSF14(3), TNFSF15(3), TNFSF18(1), TNFSF4(1), TNFSF8(1), TPO(11), TSLP(2), VEGFA(2), VEGFB(2), VEGFC(6), XCL2(1), XCR1(1) | 55738392 | 559 | 117 | 550 | 193 | 181 | 206 | 101 | 0 | 70 | 1 | 1.8e-08 | 4.8e-06
3 | HSA04360_AXON_GUIDANCE | Genes involved in axon guidance | ABL1, ABLIM1, ABLIM2, ABLIM3, ARHGEF12, CDC42, CDK5, CFL1, CFL2, CHP, CXCL12, CXCR4, DCC, DPYSL2, DPYSL5, EFNA1, EFNA2, EFNA3, EFNA4, EFNA5, EFNB1, EFNB2, EFNB3, EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHB1, EPHB2, EPHB3, EPHB4, EPHB6, FES, FYN, GNAI1, GNAI2, GNAI3, GSK3B, HRAS, ITGB1, KRAS, L1CAM, LIMK1, LIMK2, LRRC4C, MAPK1, MAPK3, MET, NCK1, NCK2, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NGEF, NRAS, NRP1, NTN1, NTN2L, NTN4, NTNG1, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PLXNA1, PLXNA2, PLXNA3, PLXNB1, PLXNB2, PLXNB3, PLXNC1, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PTK2, RAC1, RAC2, RAC3, RASA1, RGS3, RHOA, RHOD, RND1, ROBO1, ROBO2, ROBO3, ROCK1, ROCK2, SEMA3A, SEMA3B, SEMA3C, SEMA3D, SEMA3E, SEMA3F, SEMA3G, SEMA4A, SEMA4B, SEMA4C, SEMA4D, SEMA4F, SEMA4G, SEMA5A, SEMA5B, SEMA6A, SEMA6B, SEMA6C, SEMA6D, SEMA7A, SLIT1, SLIT2, SLIT3, SRGAP1, SRGAP2, SRGAP3, UNC5A, UNC5B, UNC5C, UNC5D | 119 | ABL1(4), ABLIM1(6), ABLIM2(4), ABLIM3(5), ARHGEF12(9), CDC42(1), CFL1(1), CXCL12(1), CXCR4(4), DPYSL2(5), DPYSL5(1), EFNA3(1), EFNA4(1), EFNA5(5), EFNB1(3), EFNB2(1), EFNB3(3), EPHA1(6), EPHA2(5), EPHA4(6), EPHA6(5), EPHA7(10), EPHA8(7), EPHB1(9), EPHB2(8), EPHB3(2), EPHB4(5), EPHB6(4), FYN(5), GNAI1(4), ITGB1(6), L1CAM(4), LIMK1(5), LIMK2(5), LRRC4C(8), MAPK1(2), MAPK3(3), MET(5), NCK1(1), NFAT5(5), NFATC1(2), NFATC2(5), NFATC3(5), NFATC4(5), NGEF(1), NRP1(1), NTN1(5), NTN4(6), NTNG1(4), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PLXNA1(2), PLXNA2(8), PLXNA3(2), PLXNB1(5), PLXNB2(2), PLXNB3(3), PLXNC1(9), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PTK2(5), RASA1(9), RGS3(10), RHOA(5), RND1(1), ROBO3(5), ROCK1(15), ROCK2(6), SEMA3A(9), SEMA3B(1), SEMA3C(3), SEMA3D(13), SEMA3E(9), SEMA3F(1), SEMA3G(4), SEMA4A(3), SEMA4B(2), SEMA4D(13), SEMA4F(9), SEMA4G(6), SEMA5A(8), SEMA5B(11), SEMA6A(2), SEMA6B(2), SEMA6C(3), SEMA6D(9), SEMA7A(2), SLIT1(11), SLIT2(15), SLIT3(9), SRGAP1(9), SRGAP2(3), SRGAP3(4), UNC5A(2), UNC5B(6), UNC5C(12), UNC5D(9) | 61310764 | 521 | 120 | 511 | 166 | 221 | 145 | 80 | 6 | 69 | 0 | 2.4e-08 | 4.8e-06
4 | HSA04510_FOCAL_ADHESION | Genes involved in focal adhesion | ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, ARHGAP5, BAD, BCAR1, BCL2, BIRC2, BIRC3, BIRC4, BRAF, CAPN2, CAV1, CAV2, CAV3, CCND1, CCND2, CCND3, CDC42, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, CRK, CRKL, CTNNB1, DIAPH1, DOCK1, EGF, EGFR, ELK1, ERBB2, FARP2, FIGF, FLNA, FLNB, FLNC, FLT1, FN1, FYN, GRB2, GRLF1, GSK3B, HGF, HRAS, IBSP, IGF1, IGF1R, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, JUN, KDR, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LOC653852, MAP2K1, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MET, MLCK, MRCL3, MRLC2, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARVA, PARVB, PARVG, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP5K1C, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PRKCA, PRKCB1, PRKCG, PTEN, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF1, RELN, RHOA, ROCK1, ROCK2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SPP1, SRC, THBS1, THBS2, THBS3, THBS4, TLN1, TLN2, TNC, TNN, TNR, TNXB, VASP, VAV1, VAV2, VAV3, VCL, VEGFA, VEGFB, VEGFC, VTN, VWF, ZYX | 180 | ACTB(2), ACTN1(5), ACTN2(8), ACTN3(3), ACTN4(3), AKT1(2), AKT2(6), AKT3(1), ARHGAP5(9), BAD(1), BCL2(1), BIRC2(4), BIRC3(7), CAPN2(6), CAV1(1), CAV2(1), CAV3(3), CCND2(1), CCND3(1), CDC42(1), CHAD(7), COL11A2(11), COL1A1(11), COL1A2(16), COL2A1(9), COL3A1(12), COL4A1(14), COL4A2(4), COL4A4(10), COL4A6(15), COL5A1(15), COL5A2(13), COL5A3(10), COL6A2(1), COL6A6(20), COMP(2), CRKL(2), DIAPH1(1), DOCK1(7), EGF(3), EGFR(11), FARP2(5), FIGF(2), FLNA(3), FLNB(16), FLNC(13), FLT1(12), FN1(21), FYN(5), GRB2(3), GRLF1(12), HGF(8), IBSP(3), IGF1(2), IGF1R(8), ITGA1(3), ITGA10(7), ITGA11(4), ITGA2(6), ITGA2B(4), ITGA3(4), ITGA4(8), ITGA5(7), ITGA6(4), ITGA7(6), ITGA8(8), ITGA9(6), ITGAV(5), ITGB1(6), ITGB3(9), ITGB4(3), ITGB5(6), ITGB6(6), ITGB7(4), ITGB8(5), KDR(10), LAMA1(24), LAMA2(25), LAMA3(18), LAMA4(11), LAMB1(8), LAMB2(5), LAMB3(9), LAMB4(16), LAMC1(11), LAMC2(10), LAMC3(8), MAP2K1(4), MAPK1(2), MAPK3(3), MAPK8(7), MAPK9(5), MET(5), MYL2(1), MYL7(1), MYL9(2), MYLK(14), MYLK2(3), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PARVA(1), PARVB(5), PARVG(3), PDGFA(1), PDGFC(3), PDGFD(3), PDGFRA(17), PDGFRB(6), PDPK1(1), PGF(2), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R2(1), PIK3R3(4), PIK3R5(1), PIP5K1C(4), PPP1CB(2), PPP1CC(2), PPP1R12A(3), PRKCA(4), PRKCG(10), PTK2(5), RAF1(6), RAP1A(2), RAP1B(2), RAPGEF1(6), RHOA(5), ROCK1(15), ROCK2(6), SHC1(3), SHC2(1), SHC3(1), SHC4(5), SOS1(7), SOS2(11), SPP1(1), SRC(3), THBS1(10), THBS2(15), THBS3(3), THBS4(2), TLN1(7), TLN2(8), TNC(16), TNN(17), TNXB(17), VASP(3), VAV1(13), VAV2(4), VAV3(12), VCL(2), VEGFA(2), VEGFB(2), VEGFC(6), VTN(6), VWF(15), ZYX(1) | 114292372 | 1039 | 158 | 1026 | 402 | 373 | 349 | 180 | 11 | 124 | 2 | 2.6e-07 | 4e-05
5 | 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 | 223 | ADCYAP1R1(2), ADORA1(8), ADORA2A(5), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(5), ADRA2A(3), ADRA2B(1), ADRB1(3), ADRB3(1), AGTR1(5), AGTR2(5), AVPR1A(4), AVPR1B(3), AVPR2(6), BDKRB2(3), BRS3(3), C3AR1(4), C5AR1(3), CALCR(5), CALCRL(6), CCKAR(2), CCKBR(5), CGA(2), CHRM1(3), CHRM3(4), CHRM4(1), CHRM5(2), CNR1(5), CRHR1(2), CRHR2(5), CTSG(3), CYSLTR1(3), CYSLTR2(4), DRD1(1), DRD2(5), DRD3(3), DRD5(6), EDNRA(4), F2(3), F2RL1(1), F2RL2(3), FPR1(2), FSHB(2), FSHR(7), GABBR1(6), GABBR2(7), GABRA1(4), GABRA2(9), GABRA3(5), GABRA4(8), GABRA6(5), GABRB1(7), GABRB2(7), GABRB3(9), GABRE(5), GABRG2(11), GABRG3(5), GABRP(4), GABRQ(8), GABRR1(2), GABRR2(4), GALR1(2), GH1(2), GH2(3), GHR(6), GHRHR(2), GHSR(5), GLP1R(7), GLP2R(5), GLRA1(2), GLRA2(3), GLRA3(8), GLRB(7), GNRHR(4), GPR156(8), GPR50(5), GPR63(4), GPR83(1), GRIA2(13), GRIA3(8), GRID2(12), GRIK1(5), GRIK2(14), GRIK4(12), GRIK5(6), GRIN1(1), GRIN2B(10), GRIN2C(4), GRIN2D(5), GRIN3A(6), GRM1(12), GRM2(4), GRM3(7), GRM4(7), GRM5(11), GRM6(10), GRM8(9), GRPR(3), GZMA(3), HCRTR1(1), HCRTR2(1), HRH1(1), HRH2(4), HRH4(2), HTR1A(5), HTR1B(5), HTR1D(2), HTR1F(2), HTR2A(3), HTR2B(1), HTR2C(8), HTR4(3), HTR5A(5), HTR7(7), LEP(1), LEPR(9), LHB(1), LHCGR(4), LTB4R(1), MAS1(2), MC2R(5), MC3R(1), MC4R(4), MC5R(6), MCHR1(6), MCHR2(3), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(9), NPBWR1(3), NPFFR2(4), NPY1R(4), NPY2R(5), NPY5R(2), NR3C1(4), NTSR1(1), OPRD1(1), OPRK1(5), OPRM1(3), OXTR(3), P2RX1(1), P2RX2(2), P2RX3(2), P2RX4(3), P2RX5(1), P2RX7(3), P2RY1(6), P2RY13(2), P2RY14(6), P2RY2(3), P2RY4(6), P2RY6(1), PARD3(7), PPYR1(4), PRL(3), PRLR(4), PRSS1(3), PRSS2(1), PRSS3(4), PTAFR(1), PTGDR(1), PTGER2(1), PTGER3(7), PTGFR(7), PTGIR(1), PTH2R(7), RXFP1(3), RXFP2(10), SCTR(3), SSTR1(5), SSTR2(3), SSTR4(4), TAAR1(4), TAAR2(2), TAAR5(6), TAAR6(5), TAAR8(2), TAAR9(3), TACR1(2), TACR2(1), TACR3(7), THRA(2), THRB(4), TRHR(8), TRPV1(4), TSHB(1), TSHR(7), VIPR1(4), VIPR2(3) | 68090504 | 831 | 146 | 822 | 318 | 316 | 276 | 162 | 9 | 68 | 0 | 3.5e-07 | 0.000043
6 | GPCRDB_CLASS_A_RHODOPSIN_LIKE |  | ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA1D, ADRA2A, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCBP2, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCRL1, CCRL2, CHML, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CMKLR1, CMKOR1, CNR1, CNR2, CX3CR1, CXCR3, CXCR4, DRD1, DRD2, DRD3, DRD4, DRD5, EDNRA, EDNRB, ELA3A, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHR, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GPR10, GPR147, GPR17, GPR173, GPR174, GPR23, GPR24, GPR27, GPR3, GPR30, GPR35, GPR37, GPR37L1, GPR4, GPR44, GPR50, GPR6, GPR63, GPR74, GPR77, GPR83, GPR85, GPR87, GPR92, GRPR, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, HTR7, LOC93164, IL8RA, IL8RB, LHCGR, LTB4R, MAS1, MC1R, MC3R, MC4R, MC5R, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPN1SW, OPN3, OPRD1, OPRK1, OPRL1, OPRM1, OR10A5, OR11A1, OR12D3, OR1C1, OR1F1, OR1Q1, OR2H1, OR5V1, OR5V1, OR12D3, OR7A5, OR7C1, OR8B8, OXTR, P2RY1, P2RY10, P2RY11, P2RY12, P2RY13, P2RY14, P2RY2, P2RY5, P2RY6, PPYR1, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, Rgr, RGR, RHO, RRH, SSTR1, SSTR2, SSTR3, SSTR4, SUCNR1, TBXA2R, TRHR | 156 | ADORA1(8), ADORA2A(5), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(5), ADRA1D(2), ADRA2A(3), ADRB1(3), ADRB3(1), AGTR1(5), AGTR2(5), AVPR1A(4), AVPR1B(3), AVPR2(6), BDKRB2(3), BRS3(3), C3AR1(4), CCKAR(2), CCKBR(5), CCR1(5), CCR3(4), CCR4(1), CCR5(1), CCR6(2), CCR7(3), CCR8(4), CCR9(6), CCRL1(5), CHML(5), CHRM1(3), CHRM3(4), CHRM4(1), CHRM5(2), CMKLR1(2), CNR1(5), CX3CR1(2), CXCR4(4), DRD1(1), DRD2(5), DRD3(3), DRD5(6), EDNRA(4), F2RL1(1), F2RL2(3), FPR1(2), FSHR(7), GALR1(2), GALT(2), GHSR(5), GPR17(1), GPR173(2), GPR174(3), GPR37(7), GPR37L1(3), GPR4(1), GPR50(5), GPR6(6), GPR63(4), GPR77(2), GPR83(1), GPR85(1), GPR87(5), GRPR(3), HCRTR1(1), HCRTR2(1), HRH1(1), HRH2(4), HTR1A(5), HTR1B(5), HTR1D(2), HTR1F(2), HTR2A(3), HTR2B(1), HTR2C(8), HTR4(3), HTR5A(5), HTR7(7), LHCGR(4), LTB4R(1), MAS1(2), MC3R(1), MC4R(4), MC5R(6), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(9), NPY1R(4), NPY2R(5), NPY5R(2), NTSR1(1), OPN1SW(3), OPN3(1), OPRD1(1), OPRK1(5), OPRM1(3), OR12D3(4), OR1C1(3), OR1F1(2), OR2H1(4), OR5V1(3), OR7A5(3), OR8B8(3), OXTR(3), P2RY1(6), P2RY12(4), P2RY13(2), P2RY14(6), P2RY2(3), P2RY6(1), PPYR1(4), PTAFR(1), PTGDR(1), PTGER2(1), PTGFR(7), PTGIR(1), RGR(3), RHO(3), RRH(4), SSTR1(5), SSTR2(3), SSTR4(4), SUCNR1(2), TRHR(8) | 38211344 | 424 | 117 | 424 | 149 | 168 | 148 | 75 | 3 | 30 | 0 | 7.7e-06 | 0.00078
7 | 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 | 160 | ADCY1(8), ADCY3(2), ADCY4(9), ADCY7(4), ADCY8(12), ADCY9(6), ADORA2A(5), ADORA2B(1), ADRA1A(5), ADRA1B(5), ADRA1D(2), ADRB1(3), ADRB3(1), AGTR1(5), ATP2A1(6), ATP2A2(6), ATP2A3(4), ATP2B1(9), ATP2B2(11), ATP2B3(4), ATP2B4(8), AVPR1A(4), AVPR1B(3), BDKRB2(3), CACNA1A(17), CACNA1B(11), CACNA1C(12), CACNA1D(8), CACNA1E(21), CACNA1F(14), CACNA1G(10), CACNA1H(2), CACNA1I(5), CACNA1S(14), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CAMK4(3), CCKAR(2), CCKBR(5), CD38(2), CHRM1(3), CHRM3(4), CHRM5(2), CHRNA7(1), CYSLTR1(3), CYSLTR2(4), DRD1(1), EDNRA(4), EGFR(11), GNA11(1), GNA14(6), GNA15(3), GNAL(4), GNAQ(4), GNAS(6), GRIN1(1), GRIN2C(4), GRIN2D(5), GRM1(12), GRM5(11), GRPR(3), HRH1(1), HRH2(4), HTR2A(3), HTR2B(1), HTR2C(8), HTR4(3), HTR5A(5), HTR7(7), ITPKB(4), ITPR1(19), ITPR2(18), ITPR3(12), LHCGR(4), MYLK(14), MYLK2(3), NOS1(11), NOS3(2), NTSR1(1), OXTR(3), P2RX1(1), P2RX2(2), P2RX3(2), P2RX4(3), P2RX5(1), P2RX7(3), PDE1A(4), PDE1B(3), PDE1C(9), PDGFRA(17), PDGFRB(6), PHKA1(8), PHKA2(6), PHKB(6), PHKG2(3), PLCB1(8), PLCB2(3), PLCB3(4), PLCB4(10), PLCD1(7), PLCD3(2), PLCD4(2), PLCE1(9), PLCG1(4), PLCG2(13), PLCZ1(4), PLN(1), PPID(3), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PRKACA(1), PRKACB(1), PRKACG(3), PRKCA(4), PRKCG(10), PRKX(2), PTAFR(1), PTGER3(7), PTGFR(7), PTK2B(1), RYR1(25), RYR2(59), RYR3(42), SLC25A4(1), SLC25A5(1), SLC8A1(13), SLC8A2(4), SLC8A3(7), SPHK1(1), SPHK2(1), TACR1(2), TACR2(1), TACR3(7), TNNC2(1), TRHR(8), TRPC1(6), VDAC1(1), VDAC3(1) | 87738276 | 852 | 158 | 843 | 333 | 361 | 260 | 148 | 5 | 75 | 3 | 9.8e-06 | 0.00078
8 | HSA04512_ECM_RECEPTOR_INTERACTION | Genes involved in ECM-receptor interaction | AGRN, CD36, CD44, CD47, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, DAG1, FN1, FNDC1, FNDC3A, FNDC4, FNDC5, GP1BA, GP1BB, GP5, GP6, GP9, HMMR, HSPG2, IBSP, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, RELN, SDC1, SDC2, SDC3, SDC4, SPP1, SV2A, SV2B, SV2C, THBS1, THBS2, THBS3, THBS4, TNC, TNN, TNR, TNXB, VTN, VWF | 82 | AGRN(1), CD36(1), CD44(3), CD47(3), CHAD(7), COL11A2(11), COL1A1(11), COL1A2(16), COL2A1(9), COL3A1(12), COL4A1(14), COL4A2(4), COL4A4(10), COL4A6(15), COL5A1(15), COL5A2(13), COL5A3(10), COL6A2(1), COL6A6(20), DAG1(5), FN1(21), FNDC1(23), FNDC3A(7), FNDC4(1), GP1BA(1), GP5(6), GP6(2), HMMR(6), HSPG2(9), IBSP(3), ITGA1(3), ITGA10(7), ITGA11(4), ITGA2(6), ITGA2B(4), ITGA3(4), ITGA4(8), ITGA5(7), ITGA6(4), ITGA7(6), ITGA8(8), ITGA9(6), ITGAV(5), ITGB1(6), ITGB3(9), ITGB4(3), ITGB5(6), ITGB6(6), ITGB7(4), ITGB8(5), LAMA1(24), LAMA2(25), LAMA3(18), LAMA4(11), LAMB1(8), LAMB2(5), LAMB3(9), LAMB4(16), LAMC1(11), LAMC2(10), LAMC3(8), SDC1(1), SDC2(3), SDC3(3), SDC4(1), SPP1(1), SV2A(5), SV2B(6), SV2C(4), THBS1(10), THBS2(15), THBS3(3), THBS4(2), TNC(16), TNN(17), TNXB(17), VTN(6), VWF(15) | 69408448 | 641 | 131 | 635 | 270 | 225 | 226 | 104 | 9 | 76 | 1 | 0.000011 | 0.00078
9 | HSA04350_TGF_BETA_SIGNALING_PATHWAY | Genes involved in TGF-beta signaling pathway | ACVR1, ACVR1B, ACVR1C, ACVR2A, ACVR2B, ACVRL1, AMH, AMHR2, BMP2, BMP4, BMP5, BMP6, BMP7, BMP8A, BMP8B, BMPR1A, BMPR1B, BMPR2, CDKN2B, CHRD, COMP, CREBBP, CUL1, DCN, E2F4, E2F5, EP300, FST, GDF5, GDF6, GDF7, hCG_1982709, ID1, ID2, ID3, ID4, IFNG, INHBA, INHBB, INHBC, INHBE, LEFTY1, LEFTY2, LTBP1, MAPK1, MAPK3, MYC, NODAL, NOG, PITX2, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, RBL1, RBL2, RBX1, RHOA, ROCK1, ROCK2, RPS6KB1, RPS6KB2, SKP1, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, SMAD6, SMAD7, SMAD9, SMURF1, SMURF2, SP1, TFDP1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, THBS1, THBS2, THBS3, THBS4, TNF, ZFYVE16, ZFYVE9 | 82 | ACVR1(4), ACVR1C(3), ACVR2B(4), ACVRL1(4), AMHR2(2), BMP2(1), BMP4(2), BMP5(5), BMP6(3), BMP7(6), BMP8A(1), BMPR1A(4), BMPR1B(10), BMPR2(10), CHRD(5), COMP(2), CREBBP(25), CUL1(8), DCN(4), E2F4(1), E2F5(2), EP300(15), FST(3), GDF5(2), GDF6(3), IFNG(1), INHBB(1), INHBC(3), INHBE(1), LTBP1(9), MAPK1(2), MAPK3(3), NODAL(1), PITX2(2), PPP2CA(1), PPP2CB(2), PPP2R1A(4), PPP2R1B(2), PPP2R2A(1), PPP2R2C(4), RBL1(5), RBL2(8), RBX1(1), RHOA(5), ROCK1(15), ROCK2(6), RPS6KB1(3), RPS6KB2(2), SKP1(1), SMAD1(2), SMAD3(9), SMAD5(1), SMAD9(3), SMURF1(3), SMURF2(2), SP1(2), TFDP1(4), TGFB1(1), TGFB2(9), TGFBR1(9), THBS1(10), THBS2(15), THBS3(3), THBS4(2), ZFYVE16(12), ZFYVE9(10) | 31056032 | 309 | 89 | 305 | 103 | 106 | 99 | 59 | 1 | 44 | 0 | 0.000011 | 0.00078
10 | CALCIUM_REGULATION_IN_CARDIAC_CELLS |  | ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, ANXA6, ARRB1, ARRB2, ATP1A4, ATP1B1, ATP1B2, ATP1B3, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1S, CACNB1, CACNB3, CALM1, CALM2, CALM3, CALR, CAMK1, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CASQ1, CASQ2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, FXYD2, GJA1, GJA12, GJA4, GJA5, GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GNA11, GNAI2, GNAI3, GNAO1, GNAQ, GNAZ, GNB1, GNB2, GNB3, GNB4, GNB5, GNG12, GNG13, GNG2, GNG3, GNG4, GNG5, GNG7, GNGT1, GRK4, GRK5, GRK6, ITPR1, ITPR2, ITPR3, KCNB1, KCNJ3, KCNJ5, MGC11266, MYCBP, NME7, PEA15, PKIA, PKIB, PKIG, PLCB3, PLN, PRKACA, PRKACB, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCQ, PRKCZ, PRKD1, RGS1, RGS10, RGS11, RGS14, RGS16, RGS17, RGS18, RGS19, RGS2, RGS20, RGS3, RGS4, RGS5, RGS6, RGS7, RGS9, RYR1, RYR2, RYR3, SARA1, SFN, SLC8A1, SLC8A3, USP5, YWHAB, YWHAH, YWHAQ, YWHAQ, MIB1 | 135 | ADCY1(8), ADCY3(2), ADCY4(9), ADCY5(11), ADCY6(1), ADCY7(4), ADCY8(12), ADCY9(6), ADRA1A(5), ADRA1B(5), ADRA1D(2), ADRB1(3), ADRB3(1), ANXA6(3), ARRB1(1), ATP1A4(8), ATP1B1(1), ATP1B2(2), ATP2A2(6), ATP2A3(4), ATP2B1(9), ATP2B2(11), ATP2B3(4), CACNA1A(17), CACNA1B(11), CACNA1C(12), CACNA1D(8), CACNA1E(21), CACNA1S(14), CACNB1(1), CACNB3(2), CALR(1), CAMK1(3), CAMK2A(1), CAMK2B(2), CAMK2D(3), CAMK2G(2), CAMK4(3), CASQ1(2), CASQ2(4), CHRM1(3), CHRM3(4), CHRM4(1), CHRM5(2), GJA1(7), GJA4(2), GJA5(3), GJB1(3), GJB3(4), GJB4(1), GNA11(1), GNAO1(5), GNAQ(4), GNAZ(1), GNB1(1), GNB3(3), GNB4(3), GNB5(1), GNG3(2), GNG4(1), GNG7(1), GNGT1(1), GRK4(5), GRK5(4), GRK6(3), ITPR1(19), ITPR2(18), ITPR3(12), KCNB1(5), KCNJ3(6), KCNJ5(4), MIB1(3), MYCBP(1), NME7(5), PEA15(1), PKIA(1), PKIB(1), PLCB3(4), PLN(1), PRKACA(1), PRKACB(1), PRKAR1A(5), PRKAR1B(1), PRKAR2B(3), PRKCA(4), PRKCD(3), PRKCE(6), PRKCG(10), PRKCH(3), PRKCQ(5), RGS1(1), RGS10(1), RGS16(2), RGS17(2), RGS18(2), RGS2(3), RGS20(4), RGS3(10), RGS4(3), RGS5(1), RGS6(3), RGS7(6), RGS9(7), RYR1(25), RYR2(59), RYR3(42), SLC8A1(13), SLC8A3(7), USP5(4), YWHAB(2), YWHAH(1), YWHAQ(1) | 63124152 | 613 | 138 | 609 | 253 | 272 | 189 | 98 | 0 | 52 | 2 | 0.000023 | 0.0014

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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