Glioblastoma Multiforme: 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: GBM.

Number of patients in set: 276

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: GBM.final_analysis_set.maf

Significantly mutated genes (q ≤ 0.1): 266

Mutations seen in COSMIC: 446

Significantly mutated genes in COSMIC territory: 55

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

Significantly mutated genesets: 176

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

Mutation Preprocessing

Read 276 MAFs of type "Broad"

Total number of mutations in input MAFs: 36691

Mutation Filtering

Number of mutations before filtering: 36691

After removing 139 mutations outside gene set: 36552

After removing 81 mutations outside category set: 36471

After removing 233 "impossible" mutations in

gene-patient-category bins of zero coverage: 36238

Results
Breakdown of Mutations by Type

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

type | count
--- | ---
De_novo_Start_InFrame | 6
De_novo_Start_OutOfFrame | 10
Frame_Shift_Del | 814
Frame_Shift_Ins | 363
In_Frame_Del | 329
In_Frame_Ins | 38
Indel | 1
Missense_Mutation | 23575
Nonsense_Mutation | 1747
Nonstop_Mutation | 17
Silent | 8955
Splice_Site_DNP | 11
Splice_Site_Del | 102
Splice_Site_Ins | 28
Splice_Site_ONP | 1
Splice_Site_SNP | 469
Start_Codon_Del | 2
Start_Codon_Ins | 1
Stop_Codon_Del | 2
Total | 36471

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 | 8794 | 406970401 | 0.000022 | 22 | 6
*Cp(A/C/T)->T | 3993 | 3448378213 | 1.2e-06 | 1.2 | 0.32
C->(G/A) | 5881 | 3855348614 | 1.5e-06 | 1.5 | 0.43
A->mut | 4753 | 3770634164 | 1.3e-06 | 1.3 | 0.35
indel+null | 3857 | 7625982864 | 5.1e-07 | 0.51 | 0.14
double_null | 79 | 7625982864 | 1e-08 | 0.01 | 0.0029
Total | 27357 | 7625982864 | 3.6e-06 | 3.6 | 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: GBM.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: 266. 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 | PIK3R1 | phosphoinositide-3-kinase, regulatory subunit 1 (alpha) | 642722 | 17 | 17 | 14 | 0 | 0 | 3 | 2 | 4 | 8 | 0 | <1.00e-15 | 0.000013 | 0.0044 | 0.000018 | <0.00 | <0.00
2 | IDH1 | isocitrate dehydrogenase 1 (NADP+), soluble | 349470 | 15 | 15 | 2 | 0 | 14 | 0 | 1 | 0 | 0 | 0 | <1.00e-15 | 2e-07 | 0.97 | 0.000011 | <0.00 | <0.00
3 | KRTAP5-5 | keratin associated protein 5-5 | 181491 | 18 | 16 | 7 | 0 | 0 | 0 | 3 | 1 | 14 | 0 | <1.00e-15 | 0.00082 | 1 | 0.0023 | <1.11e-16 | <6.61e-13
4 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 885302 | 19 | 19 | 17 | 1 | 3 | 5 | 2 | 7 | 2 | 0 | 6.22e-15 | 0.015 | 0.0048 | 0.00068 | 2.22e-16 | 9.91e-13
5 | TP53 | tumor protein p53 | 344937 | 89 | 80 | 63 | 1 | 23 | 15 | 12 | 13 | 24 | 2 | <1.00e-15 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.05e-12
6 | EGFR | epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) | 1089173 | 58 | 54 | 26 | 5 | 9 | 21 | 23 | 5 | 0 | 0 | <1.00e-15 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.05e-12
7 | MICALCL | MICAL C-terminal like | 537385 | 13 | 13 | 3 | 0 | 0 | 0 | 0 | 1 | 12 | 0 | 2.68e-13 | 2e-07 | 0.6 | 0 | <1.00e-15 | <1.05e-12
8 | C7orf52 | chromosome 7 open reading frame 52 | 247344 | 6 | 6 | 2 | 1 | 1 | 5 | 0 | 0 | 0 | 0 | 0.00021 | 0.0017 | 4e-07 | 0 | <1.00e-15 | <1.05e-12
9 | KDSR | 3-ketodihydrosphingosine reductase | 270146 | 5 | 5 | 1 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0.000064 | 2e-07 | 0.63 | 0 | <1.00e-15 | <1.05e-12
10 | PLA2G2A | phospholipase A2, group IIA (platelets, synovial fluid) | 123007 | 5 | 5 | 1 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 1.07e-06 | 2e-07 | 0.25 | 0 | <1.00e-15 | <1.05e-12
11 | MRM1 | mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae) | 284558 | 4 | 4 | 1 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0.0011 | 4e-07 | 0.39 | 0 | <1.00e-15 | <1.05e-12
12 | CD4 | CD4 molecule | 379108 | 3 | 3 | 1 | 1 | 0 | 0 | 0 | 3 | 0 | 0 | 0.014 | 2.6e-06 | 0.00046 | 0 | <1.00e-15 | <1.05e-12
13 | SPHK2 | sphingosine kinase 2 | 414038 | 2 | 3 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0.15 | 1.2e-06 | 8.4e-06 | 0 | <1.00e-15 | <1.05e-12
14 | ACSM2B | acyl-CoA synthetase medium-chain family member 2B | 454814 | 2 | 2 | 2 | 2 | 0 | 0 | 0 | 1 | 1 | 0 | 0.099 | 0.00024 | 0.68 | 0 | <1.00e-15 | <1.05e-12
15 | C1orf100 | chromosome 1 open reading frame 100 | 126907 | 2 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.033 | 0.013 | 0.75 | 0 | <1.00e-15 | <1.05e-12
16 | TAPBPL | TAP binding protein-like | 353808 | 2 | 2 | 2 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 0.21 | 0.00055 | 0.68 | 0 | <1.00e-15 | <1.05e-12
17 | ABCA3 | ATP-binding cassette, sub-family A (ABC1), member 3 | 1218196 | 3 | 1 | 3 | 1 | 0 | 0 | 2 | 1 | 0 | 0 | 0.94 | 6e-07 | 0.012 | 0 | <1.00e-15 | <1.05e-12
18 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 314597 | 80 | 79 | 65 | 0 | 7 | 19 | 8 | 11 | 35 | 0 | <1.00e-15 | 0.039 | 0.38 | 0.064 | <2.44e-15 | <2.42e-12
19 | RB1 | retinoblastoma 1 (including osteosarcoma) | 722445 | 21 | 21 | 19 | 1 | 1 | 1 | 1 | 0 | 18 | 0 | <1.00e-15 | 0.064 | 0.38 | 0.12 | <4.55e-15 | <4.28e-12
20 | NF1 | neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) | 2380799 | 31 | 25 | 30 | 1 | 2 | 5 | 3 | 4 | 14 | 3 | 9.44e-15 | 0.47 | 0.71 | 0.64 | 2.04e-13 | 1.82e-10
21 | SPTA1 | spectrin, alpha, erythrocytic 1 (elliptocytosis 2) | 2040988 | 30 | 26 | 28 | 5 | 12 | 4 | 6 | 1 | 7 | 0 | 4.55e-14 | 0.27 | 0.29 | 0.37 | 5.49e-13 | 4.67e-10
22 | FOXRED1 | FAD-dependent oxidoreductase domain containing 1 | 345284 | 9 | 9 | 1 | 0 | 0 | 0 | 0 | 9 | 0 | 0 | 1.64e-09 | 2e-07 | 0.93 | 0.000019 | 1.01e-12 | 8.20e-10
23 | COMMD4 | COMM domain containing 4 | 147026 | 6 | 6 | 1 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 9.71e-08 | 2e-07 | 1 | 0.000015 | 4.06e-11 | 3.15e-08
24 | CRYBA2 | crystallin, beta A2 | 136089 | 6 | 6 | 3 | 1 | 0 | 0 | 5 | 1 | 0 | 0 | 1.10e-07 | 2e-07 | 0.86 | 0.000019 | 5.80e-11 | 4.31e-08
25 | RYR2 | ryanodine receptor 2 (cardiac) | 3381004 | 36 | 28 | 35 | 7 | 21 | 3 | 6 | 6 | 0 | 0 | 1.24e-10 | 0.11 | 0.37 | 0.14 | 4.61e-10 | 3.29e-07
26 | FUT7 | fucosyltransferase 7 (alpha (1,3) fucosyltransferase) | 113313 | 5 | 5 | 1 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 2.12e-06 | 2e-07 | 0.97 | 0.000015 | 8.10e-10 | 5.56e-07
27 | NRBP2 | nuclear receptor binding protein 2 | 119779 | 4 | 4 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0.000057 | 4e-07 | 0.99 | 6e-07 | 8.59e-10 | 5.68e-07
28 | HMP19 |  | 143577 | 5 | 5 | 1 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 4.88e-06 | 2e-07 | 0.93 | 0.000011 | 1.32e-09 | 8.43e-07
29 | MST1 | macrophage stimulating 1 (hepatocyte growth factor-like) | 467340 | 10 | 9 | 6 | 0 | 2 | 0 | 0 | 1 | 7 | 0 | 4.21e-09 | 0.0053 | 0.89 | 0.014 | 1.46e-09 | 8.96e-07
30 | DNASE1L1 | deoxyribonuclease I-like 1 | 189681 | 6 | 6 | 2 | 1 | 1 | 0 | 5 | 0 | 0 | 0 | 6.20e-07 | 0.0001 | 0.081 | 0.00014 | 2.13e-09 | 1.25e-06
31 | ZNF704 | zinc finger protein 704 | 335326 | 5 | 5 | 1 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0.00011 | 4e-07 | 0.91 | 8e-07 | 2.17e-09 | 1.25e-06
32 | EML2 | echinoderm microtubule associated protein like 2 | 517871 | 8 | 8 | 3 | 1 | 0 | 0 | 0 | 0 | 8 | 0 | 2.90e-06 | 0.000014 | 0.82 | 0.000038 | 2.64e-09 | 1.46e-06
33 | TMEM45A | transmembrane protein 45A | 233464 | 5 | 5 | 1 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0.000016 | 2e-07 | 0.08 | 7.2e-06 | 2.70e-09 | 1.46e-06
34 | FOXC1 | forkhead box C1 | 130178 | 4 | 4 | 3 | 1 | 0 | 0 | 3 | 1 | 0 | 0 | 0.00018 | 2e-07 | 0.94 | 8e-07 | 3.40e-09 | 1.79e-06
35 | FLG | filaggrin | 3183335 | 30 | 28 | 30 | 13 | 12 | 6 | 6 | 3 | 3 | 0 | 2.15e-09 | 0.6 | 0.044 | 0.13 | 6.61e-09 | 3.37e-06

PIK3R1

Figure S1. This figure depicts the distribution of mutations and mutation types across the PIK3R1 significant gene.

IDH1

Figure S2. This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.

KRTAP5-5

Figure S3. This figure depicts the distribution of mutations and mutation types across the KRTAP5-5 significant gene.

PIK3CA

Figure S4. This figure depicts the distribution of mutations and mutation types across the PIK3CA significant gene.

TP53

Figure S5. This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

EGFR

Figure S6. This figure depicts the distribution of mutations and mutation types across the EGFR significant gene.

MICALCL

Figure S7. This figure depicts the distribution of mutations and mutation types across the MICALCL significant gene.

C7orf52

Figure S8. This figure depicts the distribution of mutations and mutation types across the C7orf52 significant gene.

KDSR

Figure S9. This figure depicts the distribution of mutations and mutation types across the KDSR significant gene.

PLA2G2A

Figure S10. This figure depicts the distribution of mutations and mutation types across the PLA2G2A significant gene.

MRM1

Figure S11. This figure depicts the distribution of mutations and mutation types across the MRM1 significant gene.

CD4

Figure S12. This figure depicts the distribution of mutations and mutation types across the CD4 significant gene.

SPHK2

Figure S13. This figure depicts the distribution of mutations and mutation types across the SPHK2 significant gene.

ACSM2B

Figure S14. This figure depicts the distribution of mutations and mutation types across the ACSM2B significant gene.

C1orf100

Figure S15. This figure depicts the distribution of mutations and mutation types across the C1orf100 significant gene.

TAPBPL

Figure S16. This figure depicts the distribution of mutations and mutation types across the TAPBPL significant gene.

ABCA3

Figure S17. This figure depicts the distribution of mutations and mutation types across the ABCA3 significant gene.

PTEN

Figure S18. This figure depicts the distribution of mutations and mutation types across the PTEN significant gene.

RB1

Figure S19. This figure depicts the distribution of mutations and mutation types across the RB1 significant gene.

NF1

Figure S20. This figure depicts the distribution of mutations and mutation types across the NF1 significant gene.

SPTA1

Figure S21. This figure depicts the distribution of mutations and mutation types across the SPTA1 significant gene.

FOXRED1

Figure S22. This figure depicts the distribution of mutations and mutation types across the FOXRED1 significant gene.

COMMD4

Figure S23. This figure depicts the distribution of mutations and mutation types across the COMMD4 significant gene.

CRYBA2

Figure S24. This figure depicts the distribution of mutations and mutation types across the CRYBA2 significant gene.

RYR2

Figure S25. This figure depicts the distribution of mutations and mutation types across the RYR2 significant gene.

FUT7

Figure S26. This figure depicts the distribution of mutations and mutation types across the FUT7 significant gene.

NRBP2

Figure S27. This figure depicts the distribution of mutations and mutation types across the NRBP2 significant gene.

HMP19

Figure S28. This figure depicts the distribution of mutations and mutation types across the HMP19 significant gene.

MST1

Figure S29. This figure depicts the distribution of mutations and mutation types across the MST1 significant gene.

DNASE1L1

Figure S30. This figure depicts the distribution of mutations and mutation types across the DNASE1L1 significant gene.

ZNF704

Figure S31. This figure depicts the distribution of mutations and mutation types across the ZNF704 significant gene.

EML2

Figure S32. This figure depicts the distribution of mutations and mutation types across the EML2 significant gene.

TMEM45A

Figure S33. This figure depicts the distribution of mutations and mutation types across the TMEM45A significant gene.

FOXC1

Figure S34. This figure depicts the distribution of mutations and mutation types across the FOXC1 significant gene.

Note:

N - number of sequenced bases in this gene across the individual set.

n - number of (nonsilent) mutations in this gene across the individual set.

npat - number of patients (individuals) with at least one nonsilent mutation.

nsite - number of unique sites having a non-silent mutation.

nsil - number of silent mutations in this gene across the individual set.

n1 - number of nonsilent mutations of type: *CpG->T .

n2 - number of nonsilent mutations of type: *Cp(A/C/T)->T .

n3 - number of nonsilent mutations of type: C->(G/A) .

n4 - number of nonsilent mutations of type: A->mut .

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: 55. Number of genes displayed: 10

rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | IDH1 | isocitrate dehydrogenase 1 (NADP+), soluble | 15 | 3 | 15 | 828 | 22380 | 0 | 0
2 | PIK3R1 | phosphoinositide-3-kinase, regulatory subunit 1 (alpha) | 17 | 33 | 9 | 9108 | 20 | 0 | 0
3 | EGFR | epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) | 58 | 218 | 46 | 60168 | 640 | 0 | 0
4 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 80 | 728 | 79 | 200928 | 2714 | 0 | 0
5 | TP53 | tumor protein p53 | 89 | 823 | 89 | 227148 | 26312 | 0 | 0
6 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 19 | 184 | 15 | 50784 | 3911 | 0 | 0
7 | RB1 | retinoblastoma 1 (including osteosarcoma) | 21 | 267 | 11 | 73692 | 30 | 0 | 0
8 | NF1 | neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) | 31 | 285 | 10 | 78660 | 18 | 0 | 0
9 | PTPN11 | protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) | 6 | 31 | 4 | 8556 | 16 | 3.6e-08 | 0.000018
10 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 6 | 88 | 5 | 24288 | 42058 | 3.9e-08 | 0.000018

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: 176. 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 | 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 | 246 | ACVR1C(2), AKT1(1), AKT2(1), AKT3(1), ATF2(1), ATF4(1), BDNF(1), BRAF(6), CACNA1A(4), CACNA1B(7), CACNA1C(5), CACNA1D(9), CACNA1E(9), CACNA1F(10), CACNA1G(6), CACNA1H(9), CACNA1I(5), CACNA1S(12), CACNA2D1(8), CACNA2D2(1), CACNA2D3(3), CACNA2D4(1), CACNB2(1), CACNB3(1), CACNG1(1), CACNG2(1), CACNG3(4), CACNG6(1), CACNG7(1), CACNG8(1), CD14(2), CDC25B(1), CHUK(4), DAXX(4), DDIT3(1), DUSP10(1), DUSP14(1), DUSP16(1), DUSP2(2), DUSP4(3), DUSP8(1), DUSP9(1), EGF(3), EGFR(58), ELK1(1), ELK4(1), FGF10(1), FGF13(1), FGF14(2), FGF18(1), FGF2(1), FGF20(2), FGF21(1), FGF23(3), FGF3(1), FGF6(3), FGF9(1), FGFR1(3), FGFR2(3), FGFR3(2), FGFR4(3), FLNA(14), FLNB(4), FLNC(6), FOS(1), GADD45B(1), GNA12(2), IKBKB(2), IL1R1(2), KRAS(1), MAP2K1(1), MAP2K2(1), MAP2K3(1), MAP2K5(1), MAP2K7(1), MAP3K1(5), MAP3K10(3), MAP3K12(5), MAP3K13(2), MAP3K14(2), MAP3K2(1), MAP3K3(4), MAP3K4(2), MAP3K5(1), MAP3K6(5), MAP3K7(2), MAP4K1(1), MAP4K2(1), MAP4K3(1), MAP4K4(5), MAPK1(3), MAPK13(1), MAPK14(1), MAPK3(2), MAPK7(3), MAPK8IP1(3), MAPK8IP2(3), MAPK8IP3(5), MAPK9(2), MAPKAPK2(1), MAPKAPK3(1), MAPT(1), MAX(2), MEF2C(1), MKNK1(1), NF1(31), NFATC2(1), NFATC4(2), NFKB1(1), NFKB2(1), NR4A1(3), NRAS(1), NTF3(1), NTRK1(4), NTRK2(1), PAK1(2), PDGFRA(10), PDGFRB(5), PLA2G12A(3), PLA2G2A(5), PLA2G2F(2), PLA2G3(2), PLA2G4A(4), PLA2G5(1), PLA2G6(3), PPM1B(1), PPP3CB(1), PPP3R1(1), PPP3R2(1), PPP5C(1), PRKACG(1), PRKCA(3), PRKCG(1), PRKX(2), PTPRR(2), RAP1B(2), RAPGEF2(4), RASA2(1), RASGRF1(5), RASGRF2(6), RASGRP1(1), RASGRP2(2), RASGRP3(2), RASGRP4(3), RPS6KA2(2), RPS6KA3(5), RRAS2(3), SOS1(1), SOS2(4), SRF(2), STK3(2), STK4(1), STMN1(1), TAOK1(1), TAOK2(2), TAOK3(2), TGFB1(1), TGFB2(1), TGFBR1(1), TGFBR2(5), TNFRSF1A(2), TP53(89), TRAF2(2), ZAK(1) | 111569559 | 586 | 213 | 518 | 148 | 184 | 87 | 111 | 98 | 100 | 6 | <1.00e-15 | <1.37e-14
2 | HSA04115_P53_SIGNALING_PATHWAY | Genes involved in p53 signaling pathway | APAF1, ATM, ATR, BAI1, BAX, BBC3, BID, CASP3, CASP8, CASP9, CCNB1, CCNB2, CCNB3, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNG1, CCNG2, CD82, CDC2, CDK2, CDK4, CDK6, CDKN1A, CDKN2A, CHEK1, CHEK2, CYCS, DDB2, EI24, FAS, GADD45A, GADD45B, GADD45G, GTSE1, IGF1, IGFBP3, LRDD, MDM2, MDM4, P53AIP1, PERP, PMAIP1, PPM1D, PTEN, RCHY1, RFWD2, RPRM, RRM2, RRM2B, SCOTIN, SERPINB5, SERPINE1, SESN1, SESN2, SESN3, SFN, SIAH1, STEAP3, THBS1, TNFRSF10B, TP53, TP53I3, TP73, TSC2, ZMAT3 | 64 | APAF1(1), ATM(7), ATR(9), BAI1(1), BID(4), CCNB3(1), CCND2(1), CCNE1(1), CCNE2(1), CCNG1(2), CDKN1A(1), CDKN2A(3), CHEK1(5), DDB2(1), GADD45B(1), GTSE1(2), IGFBP3(1), MDM2(1), MDM4(2), PERP(3), PPM1D(1), PTEN(80), RFWD2(2), RPRM(1), SERPINB5(2), SERPINE1(1), SESN1(2), SESN2(1), SESN3(3), STEAP3(2), THBS1(3), TP53(89), TP53I3(2), TP73(1), TSC2(2) | 25535861 | 240 | 158 | 198 | 28 | 44 | 51 | 32 | 39 | 71 | 3 | <1.00e-15 | <1.37e-14
3 | ST_INTEGRIN_SIGNALING_PATHWAY | Integrins are transmembrane receptors that mediate cell growth, survival, and migration by binding to ligands in the extracellular matrix. | ABL1, ACK1, ACTN1, ACTR2, ACTR3, AKT1, AKT2, AKT3, ANGPTL2, ARHGEF6, ARHGEF7, BCAR1, BRAF, CAV1, CDC42, CDKN2A, CRK, CSE1L, DDEF1, DOCK1, EPHB2, FYN, GRAF, GRB2, GRB7, GRF2, GRLF1, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGB3BP, MAP2K4, MAP2K7, MAP3K11, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MRAS, MYLK, MYLK2, P4HB, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PKLR, PLCG1, PLCG2, PTEN, PTK2, RAF1, RALA, RHO, ROCK1, ROCK2, SHC1, SOS1, SOS2, SRC, TERF2IP, TLN1, TLN2, VASP, WAS, ZYX | 78 | ABL1(1), ACTN1(1), ACTR3(2), AKT1(1), AKT2(1), AKT3(1), ANGPTL2(2), ARHGEF7(1), BRAF(6), CAV1(1), CDKN2A(3), CSE1L(2), DOCK1(9), EPHB2(6), GRB7(1), GRLF1(4), ILK(2), ITGA1(1), ITGA10(3), ITGA11(2), ITGA2(4), ITGA3(2), ITGA4(7), ITGA5(1), ITGA6(2), ITGA7(3), ITGA8(7), ITGA9(1), MAP2K7(1), MAPK1(3), MAPK8IP1(3), MAPK8IP2(3), MAPK8IP3(5), MAPK9(2), MYLK(7), MYLK2(1), PAK1(2), PAK3(2), PAK6(1), PAK7(3), PIK3CA(19), PIK3CB(2), PKLR(4), PLCG1(3), PLCG2(11), PTEN(80), PTK2(2), RALA(1), RHO(1), ROCK1(3), ROCK2(4), SOS1(1), SOS2(4), SRC(2), TERF2IP(3), TLN1(6), TLN2(5), VASP(2), ZYX(2) | 48062722 | 265 | 143 | 245 | 58 | 68 | 49 | 41 | 50 | 57 | 0 | <1.00e-15 | <1.37e-14
4 | ST_FAS_SIGNALING_PATHWAY | The Fas receptor induces apoptosis and NF-kB activation when bound to Fas ligand. | ADPRT, ALG2, BAK1, BAX, BFAR, BIRC4, BTK, CAD, CASP10, CASP3, CASP8, CASP8AP2, CD7, CDK2AP1, CSNK1A1, DAXX, DEDD, DEDD2, DFFA, DIABLO, EGFR, EPHB2, FADD, FAF1, FAIM2, FREQ, HRB, HSPB1, IL1A, IL8, MAP2K4, MAP2K7, MAP3K1, MAP3K5, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MCP, MET, NFAT5, NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIE, NFKBIL1, NFKBIL2, NR0B2, PFN1, PFN2, PTPN13, RALBP1, RIPK1, ROCK1, SMPD1, TNFRSF6, TNFRSF6B, TP53, TPX2, TRAF2, TUFM, VIL2 | 59 | BTK(1), CAD(6), CASP8AP2(3), CD7(2), DAXX(4), DEDD2(2), DFFA(1), DIABLO(1), EGFR(58), EPHB2(6), FAF1(3), FAIM2(1), MAP2K7(1), MAP3K1(5), MAP3K5(1), MAPK1(3), MAPK8IP1(3), MAPK8IP2(3), MAPK8IP3(5), MAPK9(2), MET(5), NFAT5(3), NFKB1(1), NFKB2(1), NFKBIA(2), NFKBIB(1), NFKBIE(1), NFKBIL1(1), NFKBIL2(6), NR0B2(3), PTPN13(4), RALBP1(3), RIPK1(1), ROCK1(3), TNFRSF6B(2), TP53(89), TPX2(1), TRAF2(2), TUFM(1) | 28393004 | 241 | 142 | 182 | 36 | 57 | 53 | 55 | 36 | 38 | 2 | <1.00e-15 | <1.37e-14
5 | SIG_CHEMOTAXIS | Genes related to chemotaxis | ACTR2, ACTR3, AKT1, AKT2, AKT3, ANGPTL2, ARHGAP1, ARHGAP4, ARHGEF11, BTK, CDC42, CFL1, CFL2, GDI1, GDI2, INPPL1, ITPR1, ITPR2, ITPR3, LIMK1, MYLK, MYLK2, P101-PI3K, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDK1, PIK3CA, PIK3CD, PIK3CG, PIK3R1, PITX2, PPP1R13B, PTEN, RACGAP1, RHO, ROCK1, ROCK2, RPS4X, SAG, WASF1, WASL | 44 | ACTR3(2), AKT1(1), AKT2(1), AKT3(1), ANGPTL2(2), ARHGAP1(1), ARHGAP4(1), ARHGEF11(3), BTK(1), CFL2(1), INPPL1(4), ITPR1(7), ITPR2(11), ITPR3(11), LIMK1(1), MYLK(7), MYLK2(1), PAK1(2), PAK3(2), PAK6(1), PAK7(3), PIK3CA(19), PIK3CD(2), PIK3CG(12), PIK3R1(17), PTEN(80), RACGAP1(1), RHO(1), ROCK1(3), ROCK2(4), RPS4X(1), WASF1(1) | 27707675 | 205 | 139 | 185 | 32 | 44 | 40 | 31 | 32 | 58 | 0 | <1.00e-15 | <1.37e-14
6 | TELPATHWAY | Telomerase is a ribonucleotide protein that adds telomeric repeats to the 3' ends of chromosomes. | AKT1, BCL2, EGFR, G22P1, HSPCA, IGF1R, KRAS2, MYC, POLR2A, PPP2CA, PRKCA, RB1, TEP1, TERF1, TERT, TNKS, TP53, XRCC5 | 15 | AKT1(1), BCL2(3), EGFR(58), IGF1R(2), POLR2A(2), PPP2CA(1), PRKCA(3), RB1(21), TEP1(4), TERT(8), TNKS(4), TP53(89), XRCC5(1) | 11328048 | 197 | 139 | 135 | 11 | 45 | 40 | 42 | 22 | 46 | 2 | <1.00e-15 | <1.37e-14
7 | 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 | 79 | AIFM1(4), AKT1(1), AKT2(1), AKT3(1), APAF1(1), ATM(7), BCL2(3), BID(4), BIRC2(1), BIRC3(1), CAPN1(5), CAPN2(1), CASP6(1), CHUK(4), CSF2RB(4), DFFA(1), DFFB(3), IKBKB(2), IL1R1(2), IL1RAP(2), IRAK1(2), IRAK2(3), IRAK3(2), IRAK4(2), MAP3K14(2), NFKB1(1), NFKB2(1), NFKBIA(2), NTRK1(4), PIK3CA(19), PIK3CB(2), PIK3CD(2), PIK3CG(12), PIK3R1(17), PIK3R2(5), PIK3R5(2), PPP3CB(1), PPP3R1(1), PPP3R2(1), PRKACG(1), PRKAR2A(1), PRKAR2B(1), RIPK1(1), TNFRSF10A(2), TNFRSF1A(2), TNFSF10(5), TP53(89), TRAF2(2) | 32877178 | 234 | 133 | 199 | 39 | 59 | 40 | 36 | 53 | 44 | 2 | <1.00e-15 | <1.37e-14
8 | HSA00562_INOSITOL_PHOSPHATE_METABOLISM | Genes involved in inositol phosphate metabolism | CARKL, FN3K, IMPA1, IMPA2, INPP1, INPP4A, INPP4B, INPP5A, INPP5B, INPP5E, INPPL1, IPMK, ISYNA1, ITGB1BP3, ITPK1, ITPKA, ITPKB, MINPP1, MIOX, OCRL, PI4KA, PI4KB, PIB5PA, PIK3C3, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PTEN, PTPMT1, SKIP, SYNJ1, SYNJ2 | 47 | FN3K(1), IMPA1(1), INPP1(2), INPP4A(1), INPP4B(1), INPP5A(1), INPP5B(2), INPP5E(1), INPPL1(4), ITGB1BP3(2), ITPKB(2), MINPP1(1), MIOX(1), OCRL(1), PI4KA(1), PI4KB(3), PIK3C3(1), PIK3CA(19), PIK3CB(2), PIK3CD(2), PIK3CG(12), PIP4K2A(3), PIP4K2B(1), PIP4K2C(3), PIP5K1B(2), PIP5K1C(4), PLCB1(3), PLCB2(5), PLCB3(5), PLCB4(3), PLCD1(1), PLCD3(2), PLCD4(2), PLCE1(7), PLCG1(3), PLCG2(11), PLCZ1(1), PTEN(80), SYNJ1(1), SYNJ2(7) | 29194980 | 205 | 131 | 187 | 33 | 50 | 41 | 29 | 31 | 53 | 1 | <1.00e-15 | <1.37e-14
9 | 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(1), ANAPC1(4), ANAPC10(2), ANAPC11(1), ANAPC2(1), ANAPC4(2), ANAPC5(2), ATM(7), ATR(9), BUB1(4), BUB1B(1), CCNA1(1), CCNB3(1), CCND2(1), CCNE1(1), CCNE2(1), CCNH(2), CDC20(2), CDC23(1), CDC25B(1), CDC27(3), CDC7(2), CDKN1A(1), CDKN1B(3), CDKN2A(3), CDKN2B(1), CDKN2C(4), CDKN2D(1), CHEK1(5), CREBBP(8), CUL1(5), E2F2(3), E2F3(2), EP300(5), ESPL1(8), GADD45B(1), GSK3B(1), HDAC1(1), HDAC2(3), MAD1L1(1), MCM2(3), MCM3(3), MCM4(3), MCM5(1), MCM6(1), MCM7(2), MDM2(1), PCNA(1), PKMYT1(1), PLK1(1), PRKDC(5), PTTG2(2), RB1(21), RBL1(3), RBL2(1), SMAD3(1), SMAD4(1), SMC1A(7), SMC1B(3), TGFB1(1), TGFB2(1), TP53(89), YWHAB(1), YWHAE(2) | 54445600 | 261 | 130 | 233 | 42 | 53 | 45 | 52 | 32 | 76 | 3 | <1.00e-15 | <1.37e-14
10 | SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES | Genes related to the insulin receptor pathway | AKT1, AKT2, AKT3, BRD4, CAP1, CBL, CDC42, CDKN2A, F2RL2, FLOT1, FLOT2, FOXO1A, GRB2, GSK3A, GSK3B, IGFBP1, INPPL1, IRS1, IRS2, IRS4, LNPEP, MAPK1, MAPK3, PARD3, PARD6A, PDK1, PIK3CA, PIK3CD, PIK3R1, PPYR1, PSCD3, PTEN, PTPN1, RAF1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SERPINB6, SFN, SHC1, SLC2A4, SORBS1, SOS1, SOS2, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ | 48 | AKT1(1), AKT2(1), AKT3(1), BRD4(7), CBL(1), CDKN2A(3), FLOT1(2), GSK3B(1), IGFBP1(1), INPPL1(4), IRS1(4), IRS4(3), LNPEP(2), MAPK1(3), MAPK3(2), PARD3(2), PARD6A(1), PIK3CA(19), PIK3CD(2), PIK3R1(17), PPYR1(2), PTEN(80), PTPN1(1), RPS6KA2(2), RPS6KA3(5), RPS6KB1(1), SERPINB6(1), SLC2A4(3), SORBS1(2), SOS1(1), SOS2(4), YWHAB(1), YWHAE(2) | 23158627 | 182 | 128 | 162 | 32 | 30 | 35 | 21 | 36 | 60 | 0 | <1.00e-15 | <1.37e-14

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | FXRPATHWAY | The nuclear receptor transcription factors FXR and LXR are activated by cholesterol metabolites and regulate cholesterol homeostasis. | FABP6, LDLR, NR0B2, NR1H3, NR1H4, RXRA | 6 | LDLR(4), NR0B2(3), NR1H3(1), NR1H4(3), RXRA(3) | 2161711 | 14 | 15 | 15 | 3 | 3 | 2 | 4 | 3 | 2 | 0 | 0.00076 | 0.25
2 | HSA01430_CELL_COMMUNICATION | Genes involved in cell communication | ACTB, ACTG1, CHAD, COL11A1, COL11A2, COL17A1, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, DES, DSC1, DSC2, DSC3, DSG1, DSG2, DSG3, DSG4, FN1, GJA1, GJA10, GJA3, GJA4, GJA5, GJA8, GJA9, GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GJB7, GJC1, GJC2, GJC3, GJD2, GJD3, GJD4, IBSP, INA, ITGA6, ITGB4, KRT1, KRT10, KRT12, KRT13, KRT14, KRT15, KRT16, KRT17, KRT18, KRT19, KRT2, KRT20, KRT23, KRT24, KRT25, KRT27, KRT28, KRT3, KRT31, KRT32, KRT33A, KRT33B, KRT34, KRT35, KRT36, KRT37, KRT38, KRT39, KRT4, KRT40, KRT5, KRT6A, KRT6B, KRT6C, KRT7, KRT71, KRT72, KRT73, KRT74, KRT75, KRT76, KRT77, KRT78, KRT79, KRT8, KRT81, KRT82, KRT83, KRT84, KRT85, KRT86, KRT9, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LMNA, LMNB1, LMNB2, LOC728760, NES, PRPH, RELN, SPP1, THBS1, THBS2, THBS3, THBS4, TNC, TNN, TNR, TNXB, VIM, VTN, VWF | 128 | ACTB(1), CHAD(1), COL11A1(8), COL11A2(9), COL17A1(3), COL1A1(4), COL1A2(9), COL2A1(2), COL3A1(5), COL4A1(4), COL4A2(8), COL4A4(4), COL4A6(5), COL5A1(3), COL5A2(5), COL6A1(5), COL6A2(3), COL6A6(7), COMP(1), DES(3), DSC1(5), DSC2(2), DSC3(2), DSG1(4), DSG2(1), DSG3(8), DSG4(10), FN1(3), GJA1(1), GJA10(1), GJA8(1), GJA9(1), GJB1(4), GJB3(2), GJB5(2), GJB6(1), GJB7(1), GJC1(1), GJC2(1), GJC3(1), INA(2), ITGA6(2), ITGB4(5), KRT1(2), KRT10(1), KRT12(3), KRT14(3), KRT15(1), KRT16(4), KRT17(3), KRT18(3), KRT19(5), KRT2(3), KRT20(1), KRT24(1), KRT25(3), KRT28(3), KRT3(1), KRT31(3), KRT32(2), KRT33A(3), KRT33B(2), KRT34(3), KRT36(4), KRT37(2), KRT38(2), KRT4(2), KRT5(1), KRT6A(1), KRT6B(2), KRT6C(1), KRT7(3), KRT72(1), KRT73(1), KRT74(3), KRT75(2), KRT76(2), KRT77(2), KRT78(1), KRT79(2), KRT8(3), KRT81(1), KRT82(1), KRT83(2), KRT84(2), KRT85(2), KRT9(3), LAMA2(12), LAMA3(7), LAMA4(4), LAMA5(9), LAMB1(4), LAMB2(3), LAMB3(4), LAMB4(10), LAMC1(2), LAMC2(6), LAMC3(5), LMNB1(1), LMNB2(3), NES(3), RELN(20), SPP1(1), THBS1(3), THBS2(5), THBS3(1), THBS4(2), TNC(7), TNN(5), TNR(2), TNXB(6), VIM(1), VWF(10) | 89127804 | 383 | 147 | 379 | 160 | 145 | 79 | 62 | 45 | 51 | 1 | 0.00082 | 0.25
3 | TYROSINE_METABOLISM |  | ABP1, ADH1A, ADH1A, ADH1B, ADH1C, ADH1B, ADH1C, ADH4, ADH6, ADH7, ADHFE1, ALDH1A3, ALDH3A1, ALDH3B1, ALDH3B2, AOC2, AOC3, AOX1, COMT, DBH, DCT, DDC, FAH, GOT1, GOT2, GSTZ1, HGD, HPD, MAOA, MAOB, PNMT, TAT, TH, TPO, TYR | 31 | ABP1(9), ADH1A(4), ADH1B(3), ADH1C(3), ADH6(2), ADH7(1), ALDH1A3(1), ALDH3A1(3), ALDH3B1(2), ALDH3B2(1), AOC2(2), AOC3(2), AOX1(7), COMT(2), DBH(6), DDC(1), FAH(1), GOT1(1), HPD(1), MAOB(1), PNMT(1), TAT(3), TPO(4), TYR(5) | 12332970 | 66 | 42 | 65 | 14 | 35 | 9 | 9 | 13 | 0 | 0 | 0.0022 | 0.39
4 | HSA04640_HEMATOPOIETIC_CELL_LINEAGE | Genes involved in hematopoietic cell lineage | ANPEP, CD14, CD19, CD1A, CD1B, CD1C, CD1D, CD1E, CD2, CD22, CD24, CD33, CD34, CD36, CD37, CD38, CD3D, CD3E, CD3G, CD4, CD44, CD5, CD55, CD59, CD7, CD8A, CD8B, CD9, CR1, CR2, CSF1, CSF1R, CSF2, CSF2RA, CSF3, CSF3R, DNTT, EPO, EPOR, FCER2, FCGR1A, FLT3, FLT3LG, GP1BA, GP1BB, GP5, GP9, GYPA, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, IL11, IL11RA, IL1A, IL1B, IL1R1, IL1R2, IL2RA, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL7, IL7R, IL9R, ITGA1, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGAM, ITGB3, KIT, KITLG, MME, MS4A1, TFRC, THPO, TNF, TPO | 79 | ANPEP(3), CD14(2), CD19(2), CD1B(1), CD1D(2), CD1E(1), CD22(5), CD33(3), CD34(2), CD36(2), CD38(2), CD3E(1), CD3G(1), CD44(4), CD5(2), CD55(2), CD7(2), CD8A(1), CD8B(1), CD9(2), CR1(5), CR2(6), CSF1R(3), CSF3R(2), DNTT(2), EPO(1), EPOR(1), FLT3(7), FLT3LG(1), GP9(1), GYPA(1), HLA-DRA(1), HLA-DRB1(2), HLA-DRB5(2), IL1R1(2), IL2RA(3), IL4(1), IL4R(6), IL5RA(1), IL6(2), IL6R(2), IL7(1), IL7R(1), ITGA1(1), ITGA2(4), ITGA2B(2), ITGA3(2), ITGA4(7), ITGA5(1), ITGA6(2), ITGAM(8), ITGB3(1), KIT(3), KITLG(2), MS4A1(2), TFRC(2), THPO(1), TPO(4) | 31351365 | 137 | 76 | 135 | 51 | 54 | 23 | 28 | 20 | 12 | 0 | 0.0026 | 0.39
5 | BLOOD_CLOTTING_CASCADE |  | F10, F11, F12, F13B, F2, F5, F7, F8, F8A1, F9, FGA, FGB, FGG, LPA, PLG, PLAT, PLAU, PLG, SERPINB2, SERPINE1, SERPINF2, VWF | 19 | F10(1), F13B(2), F2(1), F5(9), F7(1), F8(8), FGA(3), FGB(1), FGG(4), LPA(6), PLAU(2), PLG(2), SERPINB2(2), SERPINE1(1), SERPINF2(1), VWF(10) | 13638969 | 54 | 40 | 54 | 22 | 19 | 9 | 11 | 5 | 10 | 0 | 0.0032 | 0.39
6 | CTLPATHWAY | Cytotoxic T lymphocytes induce apoptosis in infected cells presenting antigen-MHC-I complexes via the perforin and Fas/Fas ligand pathways. | B2M, CD3D, CD3E, CD3G, CD3Z, GZMB, HLA-A, ICAM1, ITGAL, ITGB2, PRF1, TNFRSF6, TNFSF6, TRA@, TRB@ | 10 | B2M(2), CD3E(1), CD3G(1), GZMB(3), HLA-A(1), ITGAL(4), ITGB2(5), PRF1(3) | 3417489 | 20 | 15 | 20 | 14 | 6 | 1 | 4 | 1 | 8 | 0 | 0.0052 | 0.44
7 | PEPTIDE_GPCRS |  | AGTR1, AGTR2, ATP8A1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CX3CR1, CXCR3, CXCR4, CXCR6, EDNRA, EDNRB, ELA3A, FPR1, FPRL1, FPRL2, FSHR, FY, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GNRHR, GPR77, GRPR, IL8RA, IL8RB, LHCGR, MC1R, MC2R, MC3R, MC4R, MC5R, NMBR, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, PPYR1, SSTR1, SSTR2, SSTR3, SSTR4, TAC4, TACR1, TACR2, TACR3, TRHR, TSHR | 64 | AGTR1(2), AGTR2(1), ATP8A1(3), AVPR1A(3), AVPR1B(1), BDKRB1(1), BDKRB2(3), BRS3(2), C3AR1(1), CCKAR(3), CCKBR(2), CCR1(2), CCR10(1), CCR3(2), CCR4(1), CCR6(2), CCR7(2), CCR8(1), CX3CR1(2), CXCR3(2), CXCR6(1), EDNRA(1), EDNRB(1), FPR1(1), FSHR(1), GALR1(3), GALR2(1), GALT(1), GHSR(4), GNB2L1(1), GRPR(1), LHCGR(1), MC2R(1), MC3R(6), MC4R(3), MC5R(2), NPY5R(4), NTSR1(2), OPRK1(1), OPRL1(2), OPRM1(4), OXTR(2), PPYR1(2), SSTR2(1), SSTR3(2), SSTR4(4), TACR1(1), TACR3(4), TRHR(2), TSHR(1) | 19940026 | 98 | 57 | 98 | 38 | 43 | 19 | 18 | 14 | 4 | 0 | 0.0053 | 0.44
8 | HSA00040_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS | Genes involved in pentose and glucuronate interconversions | AKR1B1, DCXR, GUSB, RPE, UGDH, UGP2, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT2A1, UGT2A3, UGT2B10, UGT2B11, UGT2B15, UGT2B17, UGT2B28, UGT2B4, UGT2B7, XYLB | 23 | GUSB(3), RPE(1), UGP2(1), UGT1A1(1), UGT1A10(1), UGT1A3(1), UGT1A5(2), UGT1A6(2), UGT1A9(1), UGT2A1(5), UGT2A3(3), UGT2B10(1), UGT2B11(3), UGT2B17(1), UGT2B4(5), UGT2B7(3), XYLB(4) | 9403844 | 38 | 28 | 38 | 16 | 11 | 6 | 8 | 10 | 3 | 0 | 0.0057 | 0.44
9 | NEUROTRANSMITTERSPATHWAY | Biosynthesis of neurotransmitters | DBH, GAD1, HDC, PNMT, TH, TPH1 | 6 | DBH(6), GAD1(4), HDC(3), PNMT(1), TPH1(3) | 2333567 | 17 | 13 | 17 | 6 | 10 | 4 | 2 | 1 | 0 | 0 | 0.0074 | 0.46
10 | 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 | 158 | ADORA1(2), ADORA2B(1), ADORA3(1), ADRA1D(1), ADRA2C(4), ADRB1(1), ADRB2(1), AGTR1(2), AGTR2(1), AVPR1A(3), AVPR1B(1), BDKRB1(1), BDKRB2(3), BRS3(2), C3AR1(1), CCBP2(1), CCKAR(3), CCKBR(2), CCR1(2), CCR10(1), CCR3(2), CCR4(1), CCR6(2), CCR7(2), CCR8(1), CCR9(2), CHML(2), CHRM2(4), CHRM3(3), CMKLR1(1), CNR1(2), CNR2(3), CX3CR1(2), CXCR3(2), DRD1(2), DRD2(1), DRD3(1), DRD5(4), EDNRA(1), EDNRB(1), F2RL3(1), FPR1(1), FSHR(1), GALR1(3), GALR2(1), GALT(1), GHSR(4), GNB2L1(1), GPR17(1), GPR174(1), GPR27(3), GPR3(1), GPR37(3), GPR4(1), GPR50(3), GPR6(5), GPR83(4), GPR87(1), GRPR(1), HCRTR1(2), HCRTR2(1), HRH1(1), HRH2(5), HRH3(1), HTR1A(2), HTR1B(3), HTR1D(1), HTR1E(2), HTR1F(2), HTR2A(1), HTR2C(2), HTR4(1), HTR5A(4), HTR6(1), HTR7(1), LHCGR(1), MC3R(6), MC4R(3), MC5R(2), MLNR(1), NMUR1(2), NMUR2(5), NPY5R(4), NTSR1(2), OPN1SW(2), OPRK1(1), OPRL1(2), OPRM1(4), OR1F1(2), OR1Q1(1), OR2H1(4), OR7A5(1), OR7C1(1), OXTR(2), P2RY1(1), P2RY10(1), P2RY13(3), P2RY14(1), P2RY2(2), P2RY6(2), PPYR1(2), PTAFR(2), PTGDR(1), PTGER2(2), PTGER4(2), PTGFR(2), PTGIR(1), RHO(1), RRH(1), SSTR2(1), SSTR3(2), SSTR4(4), TRHR(2) | 46757547 | 219 | 105 | 217 | 84 | 99 | 27 | 38 | 40 | 15 | 0 | 0.0076 | 0.46

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)
Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle