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

Significantly mutated genes (q ≤ 0.1): 283

Mutations seen in COSMIC: 739

Significantly mutated genes in COSMIC territory: 29

Genes with clustered mutations (&le 3 aa apart): 1771

Significantly mutated genesets: 232

Significantly mutated genesets: (excluding sig. mutated genes): 60

Results
Breakdown of Mutations by Type

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

type | count
--- | ---
De_novo_Start_InFrame | 22
De_novo_Start_OutOfFrame | 158
Frame_Shift_Del | 1290
Frame_Shift_Ins | 916
In_Frame_Del | 166
In_Frame_Ins | 28
Indel | 1
Missense_Mutation | 54509
Nonsense_Mutation | 5082
Nonstop_Mutation | 12
Read-through | 34
Silent | 19249
Splice_Site | 192
Start_Codon_DNP | 2
Total | 81661

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 | 20515 | 369939104 | 0.000055 | 55 | 6
*Cp(A/C/T)->mut | 21186 | 3041594232 | 7e-06 | 7 | 0.75
A->mut | 12242 | 3284997724 | 3.7e-06 | 3.7 | 0.4
*CpG->(G/A) | 568 | 369939104 | 1.5e-06 | 1.5 | 0.16
indel+null | 7593 | 6696531284 | 1.1e-06 | 1.1 | 0.12
double_null | 308 | 6696531284 | 4.6e-08 | 0.046 | 0.0049
Total | 62412 | 6696531284 | 9.3e-06 | 9.3 | 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.

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: 283. Number of genes displayed: 35

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 | 1.55e-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 | <1.50e-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 | 5.62e-13 | 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 | 0.62 | 3.6e-06 | 3.6e-06 | 0 | <1.00e-15 | <1.50e-12
11 | OSTN | osteocrin | 92736 | 3 | 3 | 2 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0.053 | 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 | 0.57 | 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 | 1.67e-14 | 0.0086 | 0.12 | 0.0094 | 5.88e-15 | 8.16e-12
14 | LRP1B | low density lipoprotein-related protein 1B (deleted in tumors) | 3172736 | 76 | 39 | 74 | 18 | 11 | 34 | 23 | 0 | 5 | 3 | 1.22e-15 | 0.5 | 0.79 | 0.6 | 2.64e-14 | 3.40e-11
15 | TCF7L2 | transcription factor 7-like 2 (T-cell specific, HMG-box) | 453708 | 20 | 18 | 18 | 4 | 5 | 5 | 3 | 0 | 7 | 0 | 3.46e-13 | 0.0047 | 0.096 | 0.0062 | 7.44e-14 | 8.94e-11
16 | FAT4 | FAT tumor suppressor homolog 4 (Drosophila) | 3346084 | 74 | 40 | 74 | 21 | 19 | 30 | 19 | 1 | 5 | 0 | 6.37e-10 | 0.00035 | 0.43 | 0.00086 | 1.60e-11 | 1.81e-08
17 | TTN | titin | 24865216 | 291 | 86 | 286 | 78 | 82 | 114 | 72 | 3 | 13 | 7 | 2.01e-12 | 0.53 | 0.87 | 0.58 | 3.34e-11 | 3.54e-08
18 | DMD | dystrophin (muscular dystrophy, Duchenne and Becker types) | 2608328 | 47 | 33 | 46 | 6 | 10 | 14 | 14 | 0 | 9 | 0 | 2.57e-11 | 0.04 | 0.73 | 0.074 | 5.34e-11 | 5.35e-08
19 | ACVR1B | activin A receptor, type IB | 340816 | 15 | 14 | 15 | 0 | 4 | 7 | 2 | 0 | 2 | 0 | 1.04e-08 | 0.059 | 0.00021 | 0.00065 | 1.80e-10 | 1.71e-07
20 | ARID1A | AT rich interactive domain 1A (SWI-like) | 1311268 | 22 | 21 | 20 | 3 | 2 | 5 | 1 | 1 | 13 | 0 | 1.75e-11 | 0.52 | 0.25 | 0.46 | 2.13e-10 | 1.92e-07
21 | ATM | ataxia telangiectasia mutated | 2109720 | 37 | 25 | 36 | 3 | 4 | 18 | 5 | 0 | 8 | 2 | 1.75e-10 | 0.27 | 0.17 | 0.18 | 7.91e-10 | 6.80e-07
22 | WBSCR17 | Williams-Beuren syndrome chromosome region 17 | 403312 | 19 | 19 | 18 | 3 | 10 | 5 | 1 | 0 | 3 | 0 | 3.14e-10 | 0.081 | 0.65 | 0.13 | 1.05e-09 | 8.61e-07
23 | MAP2K4 | mitogen-activated protein kinase kinase 4 | 252000 | 11 | 11 | 10 | 1 | 3 | 4 | 2 | 0 | 2 | 0 | 1.25e-08 | 0.047 | 0.032 | 0.019 | 5.52e-09 | 4.33e-06
24 | PCDH9 | protocadherin 9 | 835520 | 26 | 22 | 26 | 7 | 3 | 11 | 11 | 0 | 1 | 0 | 2.93e-10 | 0.92 | 0.88 | 1 | 6.73e-09 | 5.05e-06
25 | ZC3H13 | zinc finger CCCH-type containing 13 | 1066016 | 26 | 21 | 25 | 1 | 8 | 2 | 1 | 0 | 15 | 0 | 6.97e-10 | 0.5 | 0.35 | 0.61 | 9.65e-09 | 6.96e-06
26 | ACVR2A | activin A receptor, type IIA | 355264 | 10 | 9 | 9 | 1 | 0 | 0 | 4 | 0 | 5 | 1 | 1.79e-07 | 0.078 | 0.0074 | 0.006 | 2.32e-08 | 0.000016
27 | TNFRSF10C | tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain | 177840 | 6 | 6 | 2 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0.000055 | 5.2e-06 | 1 | 0.000034 | 3.91e-08 | 0.000026
28 | KIAA1804 |  | 540708 | 18 | 15 | 16 | 0 | 8 | 7 | 1 | 0 | 2 | 0 | 7.45e-07 | 0.0057 | 0.011 | 0.0033 | 5.19e-08 | 0.000033
29 | LIFR | leukemia inhibitory factor receptor alpha | 754200 | 24 | 18 | 24 | 5 | 4 | 6 | 9 | 1 | 4 | 0 | 1.08e-08 | 0.52 | 0.52 | 0.62 | 1.33e-07 | 0.000082
30 | SOX9 | SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) | 268720 | 10 | 10 | 10 | 0 | 0 | 0 | 1 | 0 | 8 | 1 | 1.63e-07 | 0.048 | 0.42 | 0.061 | 1.94e-07 | 0.00012
31 | KRTAP5-5 | keratin associated protein 5-5 | 131768 | 4 | 4 | 1 | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0.00032 | 0.00062 | 0.000023 | 0.000032 | 2.00e-07 | 0.00012
32 | ATP10A | ATPase, class V, type 10A | 971776 | 21 | 19 | 21 | 12 | 8 | 6 | 2 | 1 | 4 | 0 | 9.25e-07 | 0.018 | 0.69 | 0.031 | 5.23e-07 | 0.00029
33 | TXNDC3 | thioredoxin domain containing 3 (spermatozoa) | 409248 | 14 | 11 | 14 | 2 | 3 | 3 | 3 | 0 | 5 | 0 | 4.03e-08 | 0.47 | 0.82 | 0.73 | 5.42e-07 | 0.00030
34 | RAB40C | RAB40C, member RAS oncogene family | 182616 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.052 | 8e-07 | 0.22 | 1e-06 | 9.32e-07 | 0.00049
35 | PCBP1 | poly(rC) binding protein 1 | 229712 | 6 | 6 | 3 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0.0016 | 0.0015 | 0.0016 | 0.000043 | 1.18e-06 | 0.00061

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: 29. Number of genes displayed: 10

rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | APC | adenomatous polyposis coli | 187 | 838 | 137 | 187712 | 2553 | 0 | 0
2 | TP53 | tumor protein p53 | 122 | 823 | 122 | 184352 | 45406 | 0 | 0
3 | ERBB3 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | 14 | 6 | 6 | 1344 | 6 | 6.2e-14 | 9.3e-11
4 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 20 | 28 | 18 | 6272 | 17998 | 2.5e-13 | 2.8e-10
5 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 96 | 51 | 95 | 11424 | 1013913 | 4.4e-13 | 3.9e-10
6 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 23 | 88 | 20 | 19712 | 210160 | 7e-13 | 4.4e-10
7 | FBXW7 | F-box and WD repeat domain containing 7 | 45 | 91 | 31 | 20384 | 1228 | 7.1e-13 | 4.4e-10
8 | KRTAP5-5 | keratin associated protein 5-5 | 4 | 1 | 4 | 224 | 4 | 7.8e-13 | 4.4e-10
9 | SMAD4 | SMAD family member 4 | 29 | 159 | 19 | 35616 | 90 | 1.1e-12 | 5.4e-10
10 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 40 | 184 | 34 | 41216 | 13256 | 1.2e-12 | 5.4e-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

Table 5. Get Full Table Genes with Clustered Mutations

num | gene | desc | n | mindist | nmuts0 | nmuts3 | nmuts12 | npairs0 | npairs3 | npairs12
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
6684 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 96 | 0 | 2294 | 2964 | 3043 | 2294 | 2964 | 3043
13084 | TP53 | tumor protein p53 | 122 | 0 | 280 | 459 | 747 | 280 | 459 | 747
1263 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 23 | 0 | 190 | 190 | 190 | 190 | 190 | 190
648 | APC | adenomatous polyposis coli | 187 | 0 | 166 | 221 | 326 | 166 | 221 | 326
4557 | FBXW7 | F-box and WD repeat domain containing 7 | 45 | 0 | 81 | 87 | 105 | 81 | 87 | 105
9500 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 40 | 0 | 74 | 111 | 136 | 74 | 111 | 136
8433 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 20 | 0 | 61 | 73 | 73 | 61 | 73 | 73
11794 | SMAD4 | SMAD family member 4 | 29 | 0 | 24 | 30 | 56 | 24 | 30 | 56
4382 | FAM22F | family with sequence similarity 22, member F | 10 | 0 | 15 | 15 | 15 | 15 | 15 | 15
4126 | ERBB3 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) | 14 | 0 | 10 | 15 | 15 | 10 | 15 | 15

Note:

n - number of mutations in this gene in the individual set.

mindist - distance (in aa) between closest pair of mutations in this gene

npairs3 - how many pairs of mutations are within 3 aa of each other.

npairs12 - how many pairs of mutations are within 12 aa of each other.

Geneset Analyses

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 232. 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(9), 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(6), NFATC3(5), NFATC4(5), NKD1(3), NKD2(1), NLK(2), PLCB1(8), PLCB2(3), PLCB3(4), PLCB4(10), PORCN(2), PPARD(2), PPP2CA(1), PPP2CB(2), PPP2R1A(5), 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 | 898 | 218 | 762 | 158 | 276 | 207 | 133 | 8 | 221 | 53 | <1.00e-15 | <1.21e-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(2), BDKRB2(3), BRAF(23), CD14(1), CDC42(1), CFL1(1), CHRM1(3), CHRM2(11), CHRM3(4), CHRM4(1), CHRM5(2), CRKL(2), CSK(4), CYFIP1(6), CYFIP2(5), DIAPH1(1), DIAPH2(12), DIAPH3(5), DOCK1(7), EGF(3), EGFR(12), EZR(2), F2(4), F2R(1), FGD1(8), FGD3(2), FGF1(2), FGF11(3), FGF12(3), FGF13(3), FGF14(5), FGF17(1), FGF19(1), FGF20(2), FGF21(2), FGF23(1), FGF3(1), FGF5(4), FGF6(3), FGF7(1), FGF8(1), FGF9(1), FGFR1(4), FGFR2(6), FGFR3(2), FGFR4(2), FN1(22), GIT1(3), GNA12(2), GNA13(2), GRLF1(12), IQGAP1(13), IQGAP2(12), IQGAP3(12), 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(6), 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(18), TIAM2(16), TMSL3(1), VAV1(13), VAV2(4), VAV3(12), VCL(2), WAS(1), WASF1(3), WASF2(2), WASL(7) | 94731820 | 1197 | 217 | 992 | 278 | 337 | 395 | 205 | 8 | 196 | 56 | <1.00e-15 | <1.21e-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(9), CACNA1E(21), CACNA1F(14), CACNA1G(11), CACNA1H(2), CACNA1I(5), CACNA1S(15), 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(12), ELK4(2), FAS(2), FASLG(1), FGF1(2), FGF11(3), FGF12(3), FGF13(3), FGF14(5), FGF17(1), FGF19(1), FGF20(2), FGF21(2), 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(7), 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(4), 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(6), NFATC4(5), NFKB1(6), NFKB2(4), NLK(2), NR4A1(2), NRAS(20), NTF3(1), NTRK1(7), 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(4), 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 | 1157 | 213 | 971 | 313 | 406 | 378 | 217 | 10 | 140 | 6 | <1.00e-15 | <1.21e-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(12), 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(7), PIK3CA(40), PIK3CD(3), PIK3R1(10), PITX2(2), PTX3(2), RAF1(6), SRC(3) | 18222276 | 404 | 191 | 305 | 62 | 78 | 75 | 76 | 0 | 120 | 55 | <1.00e-15 | <1.21e-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 | 62 | 83 | 73 | 42 | 2 | 128 | 52 | <1.00e-15 | <1.21e-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(11), 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 | 319 | 185 | 257 | 34 | 50 | 54 | 35 | 1 | 127 | 52 | <1.00e-15 | <1.21e-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(8), 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 | 308 | 183 | 228 | 28 | 45 | 50 | 43 | 1 | 115 | 54 | <1.00e-15 | <1.21e-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(18), 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), CDKN2C(1), CHEK1(1), CHEK2(1), CREBBP(25), CUL1(9), DBF4(5), E2F2(1), E2F3(2), EP300(15), ESPL1(8), GSK3B(8), HDAC1(2), HDAC2(2), MAD1L1(2), MAD2L1(1), MAD2L2(1), MCM3(4), MCM4(4), MCM5(6), MCM6(4), MCM7(3), MDM2(4), ORC1L(1), ORC3L(1), ORC4L(1), ORC5L(1), PCNA(3), PKMYT1(1), PLK1(9), 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(2) | 46359792 | 565 | 183 | 493 | 106 | 172 | 161 | 112 | 9 | 107 | 4 | <1.00e-15 | <1.21e-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(7), 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(7), 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 | 426 | 181 | 344 | 69 | 137 | 131 | 74 | 2 | 78 | 4 | <1.00e-15 | <1.21e-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 | 59 | 69 | 53 | 28 | 0 | 115 | 53 | <1.00e-15 | <1.21e-14

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 60. 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 | 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(11), 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(1), CLDN19(1), CLDN2(1), CLDN6(2), CLDN7(2), CLDN8(5), CLDN9(1), CNTN2(7), CNTNAP1(7), CNTNAP2(12), CTLA4(2), ESAM(3), F11R(2), GLG1(4), HLA-A(3), HLA-B(3), HLA-C(2), HLA-DMA(2), HLA-DMB(2), 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(3), 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(37) | 44797856 | 448 | 107 | 438 | 174 | 155 | 151 | 79 | 3 | 56 | 4 | 6.2e-09 | 3.9e-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 | 240 | ACVR1(4), ACVR2B(5), AMHR2(2), BMP2(1), BMP7(6), BMPR1A(4), BMPR1B(10), BMPR2(11), 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(3), 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(12), FAS(2), FASLG(1), FLT1(13), 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(2), IL15RA(1), IL17A(2), IL17RA(7), 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), TNFSF13(2), TNFSF13B(1), TNFSF14(3), TNFSF15(3), TNFSF18(1), TNFSF4(1), TNFSF8(1), TPO(11), TSLP(3), VEGFA(2), VEGFB(2), VEGFC(6), XCL2(1), XCR1(1) | 55901212 | 569 | 118 | 556 | 195 | 182 | 208 | 104 | 0 | 74 | 1 | 1.5e-08 | 4.5e-06
3 | HSA04630_JAK_STAT_SIGNALING_PATHWAY | Genes involved in Jak-STAT signaling pathway | AKT1, AKT2, AKT3, BCL2L1, CBL, CBLB, CBLC, CCND1, CCND2, CCND3, CISH, CLCF1, CNTF, CNTFR, CREBBP, CRLF2, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, EP300, EPO, EPOR, GH1, GH2, GHR, GRB2, 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, IL13RA2, IL15, IL15RA, IL19, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL9, IL9R, IRF9, JAK1, JAK2, JAK3, LEP, LEPR, LIF, LIFR, MPL, MYC, OSM, OSMR, PIAS1, PIAS2, PIAS3, PIAS4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIM1, PRL, PRLR, PTPN11, PTPN6, SOCS1, SOCS2, SOCS3, SOCS4, SOCS5, SOCS7, SOS1, SOS2, SPRED1, SPRED2, SPRY1, SPRY2, SPRY3, SPRY4, STAM, STAM2, STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B, STAT6, TPO, TSLP, TYK2 | 143 | AKT1(2), AKT2(6), AKT3(1), BCL2L1(1), CBL(5), CBLB(8), CCND2(1), CCND3(1), CNTF(2), CNTFR(2), CREBBP(25), CSF2RB(7), CSF3R(10), EP300(15), GH1(2), GH2(3), GHR(6), GRB2(3), 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), IL13RA2(3), IL15(2), IL15RA(1), IL19(1), IL2(4), IL20(3), IL20RA(5), IL21(2), IL21R(5), IL22(2), IL22RA1(1), IL23R(3), IL24(2), 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), IL9(2), IRF9(3), JAK1(4), JAK2(9), JAK3(9), LEP(1), LEPR(9), MPL(2), OSM(1), OSMR(6), PIAS1(4), PIAS2(3), PIAS3(4), PIAS4(1), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R2(1), PIK3R3(4), PIK3R5(1), PIM1(1), PRL(3), PRLR(4), PTPN11(5), PTPN6(4), SOCS2(3), SOCS4(1), SOCS5(5), SOS1(7), SOS2(11), SPRED1(7), SPRED2(6), SPRY1(3), SPRY4(2), STAM(2), STAM2(2), STAT1(6), STAT2(7), STAT3(2), STAT4(3), STAT5B(3), STAT6(2), TPO(11), TSLP(3), TYK2(1) | 45825148 | 418 | 100 | 410 | 130 | 143 | 150 | 76 | 1 | 46 | 2 | 2.1e-07 | 0.000042
4 | 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(5), ACVRL1(4), AMHR2(2), BMP2(1), BMP4(2), BMP5(5), BMP6(3), BMP7(6), BMP8A(1), BMPR1A(4), BMPR1B(10), BMPR2(11), CHRD(5), COMP(2), CREBBP(25), CUL1(9), 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(5), 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 | 313 | 89 | 308 | 105 | 108 | 100 | 59 | 1 | 45 | 0 | 3e-07 | 0.000047
5 | HSA01030_GLYCAN_STRUCTURES_BIOSYNTHESIS_1 | Genes involved in glycan structures - biosynthesis 1 | A4GNT, ALG1, ALG10, ALG10B, ALG11, ALG12, ALG13, ALG14, ALG2, ALG3, ALG6, ALG8, ALG9, B3GALT6, B3GNT1, B3GNT2, B3GNT6, B3GNT7, B4GALT1, B4GALT2, B4GALT3, B4GALT4, B4GALT5, B4GALT7, C1GALT1, C1GALT1C1, ChGn, CHPF, CHST1, CHST11, CHST12, CHST13, CHST14, CHST2, CHST3, CHST4, CHST6, CHST7, CHSY-2, CHSY1, CSGlcA-T, DAD1, DDOST, DPAGT1, EXT1, EXT2, EXTL1, EXTL2, EXTL3, FUT11, FUT8, GALNAC4S-6ST, GALNACT-2, GALNT1, GALNT10, GALNT11, GALNT12, GALNT13, GALNT14, GALNT17, GALNT2, GALNT3, GALNT4, GALNT5, GALNT6, GALNT7, GALNT8, GALNT9, GALNTL1, GALNTL2, GALNTL4, GALNTL5, GANAB, GCNT1, GCNT3, GCNT4, GCS1, HS2ST1, HS3ST1, HS3ST2, HS3ST3A1, HS3ST3B1, HS3ST5, HS6ST1, HS6ST2, HS6ST3, LOC728969, MAN1A1, MAN1A2, MAN1B1, MAN1C1, MAN2A1, MGAT1, MGAT2, MGAT3, MGAT4A, MGAT4B, MGAT5, MGAT5B, NDST1, NDST2, NDST3, NDST4, OGT, RPN1, RPN2, ST3GAL1, ST3GAL2, ST3GAL3, ST3GAL4, ST6GAL1, ST6GALNAC1, STT3B, UST, WBSCR17, XYLT1, XYLT2 | 108 | A4GNT(4), ALG1(1), ALG10(3), ALG10B(8), ALG11(1), ALG12(2), ALG13(1), ALG14(1), ALG2(3), ALG3(1), ALG6(3), ALG8(6), ALG9(2), B3GNT1(2), B3GNT2(2), B3GNT7(6), B4GALT1(6), B4GALT2(3), B4GALT3(7), B4GALT5(2), C1GALT1C1(2), CHPF(3), CHST1(7), CHST11(3), CHST12(3), CHST13(2), CHST14(1), CHST2(1), CHST4(7), CHSY1(5), DAD1(2), DDOST(2), DPAGT1(2), EXT1(11), EXTL1(3), EXTL2(6), EXTL3(9), FUT11(1), FUT8(2), GALNT1(3), GALNT10(5), GALNT11(5), GALNT12(2), GALNT13(5), GALNT14(10), GALNT2(4), GALNT3(4), GALNT5(10), GALNT6(3), GALNT7(3), GALNT8(2), GALNT9(2), GALNTL1(5), GALNTL2(8), GALNTL4(2), GALNTL5(8), GANAB(4), GCNT1(5), GCNT3(4), GCNT4(7), HS2ST1(4), HS3ST1(2), HS3ST2(3), HS3ST3B1(2), HS3ST5(4), HS6ST2(2), HS6ST3(2), MAN1A1(5), MAN1A2(2), MAN1B1(2), MAN1C1(7), MAN2A1(12), MGAT1(2), MGAT3(2), MGAT4A(2), MGAT4B(1), MGAT5(3), MGAT5B(2), NDST1(4), NDST2(5), NDST3(10), NDST4(4), OGT(5), RPN2(1), ST3GAL1(1), ST3GAL2(1), ST3GAL3(4), ST3GAL4(2), ST6GAL1(1), ST6GALNAC1(3), STT3B(6), UST(1), XYLT1(7), XYLT2(2) | 36725808 | 353 | 97 | 349 | 109 | 130 | 108 | 77 | 3 | 35 | 0 | 7.9e-07 | 9e-05
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 | 157 | ADORA1(8), ADORA2A(5), ADORA2B(1), ADORA3(3), ADRA1A(5), ADRA1B(5), ADRA1D(2), ADRA2A(3), ADRB1(3), ADRB3(1), AGTR1(6), AGTR2(5), AVPR1A(4), AVPR1B(3), AVPR2(6), BDKRB2(3), BRS3(3), C3AR1(4), CCKAR(3), 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(3), CNR1(5), CX3CR1(3), CXCR4(4), DRD1(1), DRD2(5), DRD3(3), DRD5(6), EDNRA(4), F2R(1), 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(6), 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(7), MLNR(3), MTNR1B(3), NMUR1(4), NMUR2(9), NPY1R(4), NPY2R(5), NPY5R(2), NTSR1(1), NTSR2(5), 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(6), PTGIR(1), RGR(3), RHO(3), RRH(4), SSTR1(5), SSTR2(3), SSTR4(4), SUCNR1(2), TRHR(8) | 38373828 | 435 | 116 | 433 | 151 | 172 | 151 | 78 | 3 | 31 | 0 | 8.8e-07 | 9e-05
7 | HSA00240_PYRIMIDINE_METABOLISM | Genes involved in pyrimidine metabolism | AICDA, AK3, CAD, CANT1, CDA, CMPK, CTPS, CTPS2, DCK, DCTD, DHODH, DPYD, DPYS, DTYMK, DUT, ECGF1, ENTPD1, ENTPD3, ENTPD4, ENTPD5, ENTPD6, ENTPD8, ITPA, NME1, NME2, NME4, NME6, NME7, NP, NT5C, NT5C1A, NT5C1B, NT5C2, NT5C3, NT5E, NT5M, NUDT2, PNPT1, POLA1, POLA2, POLD1, POLD2, POLD3, POLD4, POLE, POLE2, POLE3, POLE4, POLR1A, POLR1B, POLR1C, POLR1D, POLR2A, POLR2B, POLR2C, POLR2D, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J, POLR2K, POLR2L, POLR3A, POLR3B, POLR3G, POLR3GL, POLR3H, POLR3K, PRIM1, PRIM2, RFC5, RRM1, RRM2, RRM2B, TK1, TK2, TXNRD1, TXNRD2, TYMS, UCK1, UCK2, UMPS, UPB1, UPP1, UPP2, UPRT, ZNRD1 | 84 | AICDA(4), AK3(1), CAD(12), CDA(1), CTPS(4), CTPS2(4), DCK(2), DCTD(3), DHODH(4), DPYS(7), DTYMK(1), ENTPD1(2), ENTPD3(5), ENTPD4(5), ENTPD5(2), ENTPD6(3), ITPA(2), NME6(4), NME7(5), NT5C1A(1), NT5C1B(10), NT5C2(4), NT5C3(2), NT5E(3), NT5M(1), PNPT1(10), POLA1(8), POLA2(2), POLD1(5), POLD2(1), POLD3(2), POLE(21), POLE2(1), POLE3(1), POLR1A(11), POLR1B(9), POLR1C(2), POLR1D(2), POLR2A(6), POLR2B(8), POLR2D(1), POLR2E(1), POLR2H(1), POLR2I(1), POLR2K(1), POLR3A(11), POLR3B(11), POLR3GL(1), POLR3H(1), POLR3K(1), RFC5(3), RRM1(2), RRM2(3), TK1(1), TK2(1), TXNRD1(3), TXNRD2(3), TYMS(3), UCK2(1), UMPS(1), UPB1(5), UPP2(2), UPRT(4) | 26661776 | 243 | 78 | 239 | 58 | 71 | 91 | 51 | 1 | 29 | 0 | 1.4e-06 | 0.00012
8 | 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 | 75 | 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(12), ERBB2(10), ERBB3(14), EREG(1), GAB1(6), GRB2(3), HBEGF(1), MAP2K1(4), MAP2K2(1), MAPK1(2), MAPK3(3), MAPK8(7), MAPK9(5), NCK1(1), NRG2(6), NRG3(7), NRG4(1), PAK1(5), PAK2(3), PAK3(5), PAK6(1), PAK7(7), PIK3CB(2), PIK3CD(3), PIK3CG(14), PIK3R2(1), PIK3R3(4), PIK3R5(1), PLCG1(4), PLCG2(13), PRKCA(4), PRKCG(10), PTK2(6), RAF1(6), RPS6KB1(3), RPS6KB2(2), SHC1(3), SHC2(1), SHC3(1), SHC4(5), SOS1(7), SOS2(11), SRC(3), STAT5B(3) | 30323256 | 268 | 93 | 256 | 86 | 98 | 84 | 49 | 4 | 33 | 0 | 2.9e-06 | 0.00022
9 | HSA00230_PURINE_METABOLISM | Genes involved in purine metabolism | ADA, ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADK, ADSL, ADSS, ADSSL1, AK1, AK2, AK3L1, AK5, AK7, ALLC, AMPD1, AMPD2, AMPD3, APRT, ATIC, CANT1, DCK, DGUOK, ECGF1, ENPP1, ENPP3, ENTPD1, ENTPD2, ENTPD3, ENTPD4, ENTPD5, ENTPD6, ENTPD8, FHIT, GART, GDA, GMPR, GMPR2, GMPS, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, GUK1, HPRT1, IMPDH1, IMPDH2, ITPA, NME1, NME2, NME4, NME6, NME7, NP, NPR1, NPR2, NT5C, NT5C1A, NT5C1B, NT5C2, NT5C3, NT5E, NT5M, NUDT2, NUDT5, NUDT9, PAICS, PAPSS1, PAPSS2, PDE10A, PDE11A, PDE1A, PDE1C, PDE2A, PDE3B, PDE4A, PDE4B, PDE4C, PDE4D, PDE5A, PDE6D, PDE6G, PDE6H, PDE7A, PDE7B, PDE8A, PDE8B, PDE9A, PFAS, PKLR, PKM2, PNPT1, POLA1, POLA2, POLD1, POLD2, POLD3, POLD4, POLE, POLE2, POLE3, POLE4, POLR1A, POLR1B, POLR1C, POLR1D, POLR2A, POLR2B, POLR2C, POLR2D, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I, POLR2J, POLR2K, POLR2L, POLR3A, POLR3B, POLR3G, POLR3GL, POLR3H, POLR3K, PPAT, PRIM1, PRIM2, PRPS1, PRPS1L1, PRPS2, PRUNE, RFC5, RRM1, RRM2, RRM2B, SAC, XDH, ZNRD1 | 140 | ADA(3), ADCY1(8), ADCY2(15), ADCY3(2), ADCY4(9), ADCY5(11), ADCY6(1), ADCY7(4), ADCY8(12), ADCY9(6), ADK(1), ADSL(7), ADSS(2), AK2(1), AK5(5), AK7(6), ALLC(5), AMPD1(9), AMPD2(5), AMPD3(3), ATIC(4), DCK(2), ENPP1(4), ENPP3(4), ENTPD1(2), ENTPD3(5), ENTPD4(5), ENTPD5(2), ENTPD6(3), FHIT(1), GART(3), GMPR(2), GMPR2(2), GMPS(5), GUCY1A2(12), GUCY1B3(9), GUCY2C(8), GUCY2D(8), GUCY2F(12), HPRT1(2), IMPDH1(2), IMPDH2(4), ITPA(2), NME6(4), NME7(5), NPR1(6), NPR2(10), NT5C1A(1), NT5C1B(10), NT5C2(4), NT5C3(2), NT5E(3), NT5M(1), NUDT9(2), PAICS(1), PAPSS1(2), PAPSS2(4), PDE10A(11), PDE11A(8), PDE1A(4), PDE1C(9), PDE3B(3), PDE4A(4), PDE4B(5), PDE4C(2), PDE4D(5), PDE5A(6), PDE6D(1), PDE7A(3), PDE7B(4), PDE8A(1), PDE8B(7), PDE9A(6), PFAS(1), PKM2(2), PNPT1(10), POLA1(8), POLA2(2), POLD1(5), POLD2(1), POLD3(2), POLE(21), POLE2(1), POLE3(1), POLR1A(11), POLR1B(9), POLR1C(2), POLR1D(2), POLR2A(6), POLR2B(8), POLR2D(1), POLR2E(1), POLR2H(1), POLR2I(1), POLR2K(1), POLR3A(11), POLR3B(11), POLR3GL(1), POLR3H(1), POLR3K(1), PPAT(6), PRPS1(1), PRPS1L1(1), PRPS2(2), PRUNE(1), RFC5(3), RRM1(2), RRM2(3), XDH(7) | 54995680 | 500 | 113 | 493 | 162 | 166 | 172 | 91 | 3 | 68 | 0 | 4.1e-06 | 0.00028
10 | 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 | 121 | 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), EPHA4(6), EPHA6(5), EPHA7(10), EPHA8(6), 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(6), 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(4), PLXNB1(5), PLXNB2(2), PLXNB3(3), PLXNC1(9), PPP3CA(3), PPP3CB(5), PPP3CC(4), PPP3R1(1), PPP3R2(1), PTK2(6), RASA1(9), RGS3(10), RHOA(5), RND1(1), 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(4), SEMA6D(9), SEMA7A(2), SLIT1(11), SLIT2(15), SLIT3(9), SRGAP1(9), SRGAP2(3), SRGAP3(4), UNC5A(2), UNC5B(6), UNC5C(12), UNC5D(9) | 63260236 | 559 | 125 | 548 | 177 | 229 | 158 | 90 | 6 | 76 | 0 | 9.4e-06 | 0.00058

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