Acute Myeloid Leukemia: Mutation Analysis (MutSig)
Maintained by Dan DiCara
(Broad Institute)
-
Overview
+
Introduction
This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v2.0 was used to generate the results found in this report.
Working with individual set: LAML.
Number of patients in set: 199
+
Input
The input for this pipeline is a set of individuals with the following files associated for each:
1. An annotated .maf file describing the mutations called for the respective individual, and their properties.
2. A .wig file that contains information about the coverage of the sample.
-
Summary
MAF used for this analysis: LAML.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 75
Mutations seen in COSMIC: 234
Significantly mutated genes in COSMIC territory: 18
Genes with clustered mutations (≤ 3 aa apart): 0
Significantly mutated genesets: 73
Significantly mutated genesets: (excluding sig. mutated genes): 0
Mutation Preprocessing
Read 199 MAFs of type "WashU"
Total number of mutations in input MAFs: 5617
After removing 98 mutations outside chr1-24: 5519
After removing 387 noncoding mutations: 5132
After collapsing adjacent/redundant mutations: 5126
Mutation Filtering
Number of mutations before filtering: 5126
After removing 640 mutations outside gene set: 4486
After removing 10 mutations outside category set: 4476
-
Results
+
Breakdown of Mutations by Type
Table 1. Get Full Table Table representing breakdown of mutations by type.
| type | count |
|---|---|
| Frame_Shift_Del | 102 |
| Frame_Shift_Ins | 118 |
| In_Frame_Del | 100 |
| In_Frame_Ins | 58 |
| Missense_Mutation | 2728 |
| Nonsense_Mutation | 191 |
| Nonstop_Mutation | 2 |
| Silent | 1073 |
| Splice_Site | 104 |
| Total | 4476 |
+
Breakdown of Mutation Rates by Category Type
Table 2. Get Full Table A breakdown of mutation rates per category discovered for this individual set.
| category | n | N | rate | rate_per_mb | relative_rate |
|---|---|---|---|---|---|
| *CpG->T | 802 | 275075312 | 2.9e-06 | 2.9 | 4.7 |
| *Cp(A/C/T)->T | 690 | 2493147819 | 2.8e-07 | 0.28 | 0.45 |
| A->G | 365 | 2773129874 | 1.3e-07 | 0.13 | 0.21 |
| transver | 869 | 5541353005 | 1.6e-07 | 0.16 | 0.26 |
| indel+null | 668 | 5541353204 | 1.2e-07 | 0.12 | 0.2 |
| double_null | 9 | 5541353204 | 1.6e-09 | 0.0016 | 0.0026 |
| Total | 3403 | 5541353204 | 6.1e-07 | 0.61 | 1 |
+
Target Coverage for Each Individual
The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).
Figure 1.
+
Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples
Figure 2. Patients counts and rates file used to generate this plot: LAML.patients.counts_and_rates.txt
+
CoMut Plot
Figure 3. Get High-res Image The matrix in the center of the figure represents individual mutations in patient samples, color-coded by type of mutation, for the significantly mutated genes. The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on the left of the matrix shows the number of mutations in each gene. The percentages represent the fraction of tumors with at least one mutation in the specified gene. The barplot to the right of the matrix displays the q-values for the most significantly mutated genes. The purple boxplots below the matrix (only displayed if required columns are present in the provided MAF) represent the distributions of allelic fractions observed in each sample. The plot at the bottom represents the base substitution distribution of individual samples, using the same categories that were used to calculate significance.
+
Significantly Mutated Genes
Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 75. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).
| rank | gene | description | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p_classic | p_ks | p_cons | p_joint | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IDH1 | isocitrate dehydrogenase 1 (NADP+), soluble | 254123 | 20 | 20 | 2 | 0 | 18 | 0 | 0 | 2 | 0 | 0 | <1.00e-15 | 2e-07 | 0.97 | 0.000011 | <0.00 | <0.00 |
| 2 | U2AF1 | U2 small nuclear RNA auxiliary factor 1 | 154822 | 10 | 10 | 3 | 0 | 0 | 6 | 0 | 4 | 0 | 0 | <1.00e-15 | 0.000026 | 0.0093 | 0.000014 | <0.00 | <0.00 |
| 3 | TET2 | tet oncogene family member 2 | 696898 | 17 | 15 | 17 | 1 | 0 | 1 | 0 | 2 | 9 | 5 | <1.00e-15 | 1 | 0.0015 | 0.006 | <2.22e-16 | <9.59e-13 |
| 4 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 140693 | 9 | 9 | 5 | 0 | 0 | 4 | 1 | 4 | 0 | 0 | <1.00e-15 | 0.0048 | 0.2 | 0.0052 | <2.22e-16 | <9.59e-13 |
| 5 | RUNX1 | runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) | 146663 | 19 | 17 | 16 | 0 | 1 | 3 | 2 | 3 | 9 | 1 | <1.00e-15 | 0.015 | 0.12 | 0.015 | <5.55e-16 | <1.33e-12 |
| 6 | WT1 | Wilms tumor 1 | 166364 | 13 | 13 | 9 | 0 | 1 | 1 | 0 | 0 | 10 | 1 | <1.00e-15 | 0.0086 | 1 | 0.019 | <7.77e-16 | <1.33e-12 |
| 7 | TP53 | tumor protein p53 | 260889 | 15 | 11 | 15 | 1 | 3 | 2 | 4 | 1 | 5 | 0 | <1.00e-15 | 0.0074 | 0.18 | 0.02 | <7.77e-16 | <1.33e-12 |
| 8 | FLT3 | fms-related tyrosine kinase 3 | 603169 | 53 | 52 | 29 | 0 | 0 | 1 | 1 | 16 | 35 | 0 | 2.33e-15 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.33e-12 |
| 9 | DNMT3A | DNA (cytosine-5-)-methyltransferase 3 alpha | 517997 | 55 | 50 | 28 | 0 | 33 | 2 | 2 | 4 | 14 | 0 | <1.00e-15 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.33e-12 |
| 10 | NPM1 | nucleophosmin (nucleolar phosphoprotein B23, numatrin) | 185269 | 47 | 47 | 1 | 0 | 0 | 0 | 0 | 0 | 47 | 0 | <1.00e-15 | 2e-07 | 2e-07 | 0 | <1.00e-15 | <1.33e-12 |
| 11 | IDH2 | isocitrate dehydrogenase 2 (NADP+), mitochondrial | 232631 | 20 | 20 | 2 | 0 | 16 | 3 | 0 | 1 | 0 | 0 | 2.00e-15 | 2e-07 | 0.62 | 0 | <1.00e-15 | <1.33e-12 |
| 12 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 116614 | 18 | 18 | 6 | 0 | 0 | 9 | 1 | 8 | 0 | 0 | 2.00e-15 | 2e-07 | 0.13 | 0 | <1.00e-15 | <1.33e-12 |
| 13 | OR5H6 | olfactory receptor, family 5, subfamily H, member 6 | 195418 | 4 | 4 | 1 | 2 | 0 | 0 | 0 | 0 | 4 | 0 | 2.06e-08 | 4e-07 | 0.034 | 0 | <1.00e-15 | <1.33e-12 |
| 14 | KIT | v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog | 591229 | 8 | 7 | 5 | 0 | 1 | 0 | 0 | 5 | 2 | 0 | 4.87e-12 | 0.011 | 0.024 | 0.0079 | 1.23e-12 | 1.52e-09 |
| 15 | PHF6 | PHD finger protein 6 | 246561 | 6 | 6 | 6 | 0 | 0 | 1 | 0 | 1 | 4 | 0 | 7.26e-13 | 0.47 | 0.067 | 0.17 | 3.80e-12 | 4.38e-09 |
| 16 | AP3S1 | adaptor-related protein complex 3, sigma 1 subunit | 106067 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 2.22e-07 | 2.8e-06 | 0.12 | 8e-07 | 5.40e-12 | 5.83e-09 |
| 17 | SCRN3 | secernin 3 | 259297 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 3.21e-07 | 8e-07 | 0.93 | 1.4e-06 | 1.32e-11 | 1.34e-08 |
| 18 | MPRIP | 375911 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 4.37e-06 | 2e-07 | 1 | 2e-07 | 2.52e-11 | 2.41e-08 | |
| 19 | CYP21A2 | cytochrome P450, family 21, subfamily A, polypeptide 2 | 205567 | 4 | 4 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 1.61e-06 | 4e-07 | 1 | 5.8e-06 | 2.46e-10 | 2.23e-07 |
| 20 | PTPN11 | protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) | 362976 | 7 | 7 | 6 | 0 | 0 | 3 | 1 | 3 | 0 | 0 | 1.68e-10 | 0.075 | 0.13 | 0.077 | 3.36e-10 | 2.90e-07 |
| 21 | ETV6 | ets variant gene 6 (TEL oncogene) | 276809 | 5 | 5 | 5 | 0 | 0 | 0 | 1 | 1 | 3 | 0 | 5.47e-10 | 0.083 | 0.067 | 0.049 | 6.80e-10 | 5.59e-07 |
| 22 | NFKBIZ | nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta | 380488 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 2.20e-06 | 0.000034 | 0.71 | 0.000034 | 1.82e-09 | 1.43e-06 |
| 23 | LILRA3 | leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3 | 268252 | 3 | 3 | 1 | 1 | 0 | 0 | 0 | 3 | 0 | 0 | 0.000032 | 1.2e-06 | 0.71 | 4.6e-06 | 3.49e-09 | 2.62e-06 |
| 24 | C17orf97 | 168553 | 5 | 5 | 4 | 1 | 0 | 0 | 1 | 4 | 0 | 0 | 3.52e-09 | 0.22 | 0.99 | 0.47 | 3.49e-08 | 0.000025 | |
| 25 | ZNF626 | zinc finger protein 626 | 326559 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.00027 | 0.0006 | 0.00048 | 2e-05 | 1.08e-07 | 0.000075 |
| 26 | MUC4 | mucin 4, cell surface associated | 1002562 | 10 | 7 | 8 | 6 | 1 | 0 | 1 | 5 | 3 | 0 | 1.24e-08 | 0.99 | 0.87 | 1 | 2.39e-07 | 0.00016 |
| 27 | SMC3 | structural maintenance of chromosomes 3 | 746449 | 6 | 6 | 6 | 0 | 1 | 1 | 1 | 1 | 2 | 0 | 2.05e-08 | 0.79 | 0.29 | 0.83 | 3.22e-07 | 0.00021 |
| 28 | ARSD | arylsulfatase D | 356608 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0.0066 | 0.00073 | 0.000078 | 3e-06 | 3.70e-07 | 0.00023 |
| 29 | NOTCH2NL | Notch homolog 2 (Drosophila) N-terminal like | 144673 | 3 | 3 | 2 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 9.67e-07 | NaN | NaN | NaN | 9.67e-07 | 0.00058 |
| 30 | PRSS16 | protease, serine, 16 (thymus) | 290142 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.000061 | 0.00068 | 0.65 | 0.0012 | 1.29e-06 | 0.00074 |
| 31 | CCDC144B | coiled-coil domain containing 144B | 212930 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.000031 | 0.00091 | 0.33 | 0.0035 | 1.82e-06 | 0.0010 |
| 32 | C16orf71 | chromosome 16 open reading frame 71 | 278600 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.00090 | 0.00071 | 0.001 | 0.00012 | 1.91e-06 | 0.0010 |
| 33 | SKA3 | 241785 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.00023 | 0.00082 | 0.37 | 0.00071 | 2.70e-06 | 0.0014 | |
| 34 | ACTRT2 | actin-related protein T2 | 188851 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.00021 | 0.0011 | 0.51 | 0.0011 | 3.66e-06 | 0.0019 |
| 35 | FAM5C | family with sequence similarity 5, member C | 463471 | 6 | 5 | 6 | 0 | 4 | 1 | 0 | 1 | 0 | 0 | 5.57e-07 | 0.74 | 0.52 | 0.85 | 7.38e-06 | 0.0036 |
Note:
N - number of sequenced bases in this gene across the individual set.
n - number of (nonsilent) mutations in this gene across the individual set.
npat - number of patients (individuals) with at least one nonsilent mutation.
nsite - number of unique sites having a non-silent mutation.
nsil - number of silent mutations in this gene across the individual set.
n1 - number of nonsilent mutations of type: *CpG->T .
n2 - number of nonsilent mutations of type: *Cp(A/C/T)->T .
n3 - number of nonsilent mutations of type: A->G .
n4 - number of nonsilent mutations of type: transver .
n5 - number of nonsilent mutations of type: indel+null .
null - mutation category that includes nonsense, frameshift, splice-site mutations
p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
+
COSMIC analyses
In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.
Table 4. Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 18. Number of genes displayed: 10
| rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q |
|---|---|---|---|---|---|---|---|---|---|
| 1 | TP53 | tumor protein p53 | 15 | 823 | 15 | 163777 | 3379 | 0 | 0 |
| 2 | IDH1 | isocitrate dehydrogenase 1 (NADP+), soluble | 20 | 3 | 20 | 597 | 29840 | 2.4e-15 | 5.3e-12 |
| 3 | IDH2 | isocitrate dehydrogenase 2 (NADP+), mitochondrial | 20 | 6 | 20 | 1194 | 2000 | 4.6e-15 | 6.6e-12 |
| 4 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 18 | 28 | 18 | 5572 | 13364 | 2.2e-14 | 1.7e-11 |
| 5 | NPM1 | nucleophosmin (nucleolar phosphoprotein B23, numatrin) | 47 | 29 | 47 | 5771 | 172819 | 2.2e-14 | 1.7e-11 |
| 6 | PTPN11 | protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1) | 7 | 31 | 6 | 6169 | 260 | 2.4e-14 | 1.7e-11 |
| 7 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 9 | 51 | 8 | 10149 | 62973 | 3.9e-14 | 2.5e-11 |
| 8 | FLT3 | fms-related tyrosine kinase 3 | 53 | 114 | 49 | 22686 | 6227 | 8.7e-14 | 4.8e-11 |
| 9 | RUNX1 | runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) | 19 | 175 | 17 | 34825 | 88 | 1.3e-13 | 5.6e-11 |
| 10 | KIT | v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog | 8 | 183 | 7 | 36417 | 3934 | 1.4e-13 | 5.6e-11 |
Note:
n - number of (nonsilent) mutations in this gene across the individual set.
cos = number of unique mutated sites in this gene in COSMIC
n_cos = overlap between n and cos.
N_cos = number of individuals times cos.
cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.
p = p-value for seeing the observed amount of overlap in this gene)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
+
Clustered Mutations
There were no clustered mutations discovered.
+
Geneset Analyses
Table 5. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 73. Number of genesets displayed: 10
| rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HSA04060_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION | Genes involved in cytokine-cytokine receptor interaction | ACVR1, ACVR1B, ACVR2A, ACVR2B, AMH, AMHR2, BMP2, BMP7, BMPR1A, BMPR1B, BMPR2, CCL1, CCL11, CCL13, CCL14, CCL15, CCL16, CCL17, CCL18, CCL19, CCL2, CCL20, CCL21, CCL22, CCL23, CCL24, CCL25, CCL26, CCL27, CCL28, CCL3, CCL4, CCL5, CCL7, CCL8, CCR1, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CD27, CD40, CD40LG, CD70, CLCF1, CNTF, CNTFR, CRLF2, CSF1, CSF1R, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, CX3CL1, CX3CR1, CXCL1, CXCL10, CXCL11, CXCL12, CXCL13, CXCL14, CXCL16, CXCL2, CXCL3, CXCL5, CXCL6, CXCL9, CXCR3, CXCR4, CXCR6, EDA, EDA2R, EDAR, EGF, EGFR, EPO, EPOR, FAS, FASLG, FLJ78302, FLT1, FLT3, FLT3LG, FLT4, GDF5, GH1, GH2, GHR, HGF, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNE1, IFNG, IFNGR1, IFNGR2, IFNK, IFNW1, IL10, IL10RA, IL10RB, IL11, IL11RA, IL12A, IL12B, IL12RB1, IL12RB2, IL13, IL13RA1, IL15, IL15RA, IL17A, IL17B, IL17RA, IL17RB, IL18, IL18R1, IL18RAP, IL19, IL1A, IL1B, IL1R1, IL1R2, IL1RAP, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL25, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL8, IL8RA, IL8RB, IL9, IL9R, INHBA, INHBB, INHBC, INHBE, KDR, KIT, KITLG, LEP, LEPR, LIF, LIFR, LOC728045, LTA, LTB, LTBR, MET, MPL, NGFR, OSM, OSMR, PDGFB, PDGFC, PDGFRA, PDGFRB, PF4, PF4V1, PLEKHO2, PPBP, PRL, PRLR, RELT, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF11A, TNFRSF11B, TNFRSF12A, TNFRSF13B, TNFRSF13C, TNFRSF14, TNFRSF17, TNFRSF18, TNFRSF19, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF4, TNFRSF6B, TNFRSF8, TNFRSF9, TNFSF10, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, TPO, TSLP, VEGFA, VEGFB, VEGFC, XCL1, XCL2, XCR1 | 242 | ACVR2B(1), CCL11(1), CCL16(1), CCL17(1), CCL20(1), CCL21(1), CD70(1), CLCF1(1), CSF3R(2), CXCL16(1), EGF(1), EGFR(2), FLT1(1), FLT3(53), GHR(1), IFNA16(1), IL1R1(1), IL23R(1), IL25(1), KDR(2), KIT(8), KITLG(1), MPL(1), PDGFRA(1), PDGFRB(1), PLEKHO2(1), TPO(1) | 50091285 | 89 | 80 | 62 | 10 | 7 | 10 | 3 | 31 | 38 | 0 | <1.00e-15 | <3.08e-14 |
| 2 | HSA04640_HEMATOPOIETIC_CELL_LINEAGE | Genes involved in hematopoietic cell lineage | ANPEP, CD14, CD19, CD1A, CD1B, CD1C, CD1D, CD1E, CD2, CD22, CD24, CD33, CD34, CD36, CD37, CD38, CD3D, CD3E, CD3G, CD4, CD44, CD5, CD55, CD59, CD7, CD8A, CD8B, CD9, CR1, CR2, CSF1, CSF1R, CSF2, CSF2RA, CSF3, CSF3R, DNTT, EPO, EPOR, FCER2, FCGR1A, FLT3, FLT3LG, GP1BA, GP1BB, GP5, GP9, GYPA, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, IL11, IL11RA, IL1A, IL1B, IL1R1, IL1R2, IL2RA, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL7, IL7R, IL9R, ITGA1, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGAM, ITGB3, KIT, KITLG, MME, MS4A1, TFRC, THPO, TNF, TPO | 83 | CR1(1), CSF3R(2), FLT3(53), IL1R1(1), ITGA4(1), KIT(8), KITLG(1), MS4A1(1), TPO(1) | 24232827 | 69 | 66 | 42 | 3 | 3 | 3 | 1 | 24 | 38 | 0 | <1.00e-15 | <3.08e-14 |
| 3 | HSA00271_METHIONINE_METABOLISM | Genes involved in methionine metabolism | AHCY, AMD1, BHMT, CBS, CTH, DNMT1, DNMT3A, DNMT3B, KIAA0828, MARS, MARS2, MAT1A, MAT2B, MTAP, MTFMT, MTR, SRM, TAT | 17 | CBS(1), DNMT1(2), DNMT3A(55), DNMT3B(2), MAT1A(1) | 5761050 | 61 | 54 | 34 | 0 | 35 | 2 | 4 | 6 | 14 | 0 | <1.00e-15 | <3.08e-14 |
| 4 | METHIONINE_METABOLISM | AHCY, BHMT, CBS, CTH, DNMT1, DNMT2, DNMT3A, DNMT3B, MARS, MARS2, MAT1A, MAT2B, MTR | 12 | CBS(1), DNMT1(2), DNMT3A(55), DNMT3B(2), MAT1A(1) | 4890226 | 61 | 54 | 34 | 0 | 35 | 2 | 4 | 6 | 14 | 0 | <1.00e-15 | <3.08e-14 | |
| 5 | ERYTHPATHWAY | Erythropoietin selectively stimulates erythrocyte differentiation from CFU-GEMM cells in bone marrow. | CCL3, CSF2, CSF3, EPO, FLT3, IGF1, IL11, IL1A, IL3, IL6, IL9, KITLG, TGFB1, TGFB2, TGFB3 | 14 | FLT3(53), KITLG(1) | 2401930 | 54 | 53 | 30 | 0 | 0 | 1 | 1 | 17 | 35 | 0 | <1.00e-15 | <3.08e-14 |
| 6 | HSA04530_TIGHT_JUNCTION | Genes involved in tight junction | ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK | 126 | CDC42(1), CGN(1), CLDN11(1), CLDN16(1), CLDN18(1), CTNNA2(1), EXOC4(1), GNAI2(1), HCLS1(1), IGSF5(1), JAM2(1), KRAS(9), LLGL2(1), MAGI1(1), MAGI2(1), MAGI3(1), MLLT4(2), MYH1(1), MYH13(2), MYH14(1), MYH15(1), MYH6(2), MYH7(2), MYL9(1), NRAS(18), PARD3(1), PPP2R1B(1), PPP2R2B(1), PPP2R3A(1), PRKCG(1), TJAP1(3), TJP1(1), TJP2(1) | 55248171 | 64 | 51 | 47 | 13 | 12 | 19 | 6 | 22 | 5 | 0 | <1.00e-15 | <3.08e-14 |
| 7 | HSA04540_GAP_JUNCTION | Genes involved in gap junction | ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRB1, CDC2, CSNK1D, DRD1, DRD2, EDG2, EGF, EGFR, GJA1, GJD2, GNA11, GNAI1, GNAI2, GNAI3, GNAQ, GNAS, GRB2, GRM1, GRM5, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, HRAS, HTR2A, HTR2B, HTR2C, ITPR1, ITPR2, ITPR3, KRAS, LOC643224, LOC654264, MAP2K1, MAP2K2, MAP2K5, MAP3K2, MAPK1, MAPK3, MAPK7, NPR1, NPR2, NRAS, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PLCB1, PLCB2, PLCB3, PLCB4, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKG1, PRKG2, PRKX, PRKY, RAF1, SOS1, SOS2, SRC, TJP1, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8 | 90 | ADCY2(1), ADCY3(1), ADCY4(2), ADCY5(1), DRD2(1), EGF(1), EGFR(2), GNAI2(1), GRM5(1), GUCY1B3(2), GUCY2C(1), GUCY2D(1), ITPR1(1), ITPR3(1), KRAS(9), MAPK1(1), NRAS(18), PDGFRA(1), PDGFRB(1), PLCB3(1), PRKCG(1), PRKG2(1), SOS1(1), TJP1(1), TUBA1A(1), TUBA1B(1), TUBA3C(2), TUBB3(1), TUBB4(1), TUBB6(1), TUBB8(1) | 37538564 | 60 | 51 | 44 | 10 | 9 | 24 | 4 | 21 | 2 | 0 | <1.00e-15 | <3.08e-14 |
| 8 | NUCLEAR_RECEPTORS | ALK, AR, ESR1, ESR2, ESRRA, HNF4A, NPM1, NR0B1, NR1D2, NR1H2, NR1H3, NR1I2, NR1I3, NR2C2, NR2E1, NR2F1, NR2F2, NR2F6, NR3C1, NR4A1, NR4A2, NR5A1, NR5A2, PGR, PPARA, PPARD, PPARG, RARA, RARB, RARG, ROR1, RORA, RORC, RXRA, RXRB, RXRG, THRA, THRA, NR1D1, THRB, VDR | 38 | NPM1(47), NR1D1(1), NR1D2(1), NR2E1(2), THRA(1), THRB(1) | 11707369 | 53 | 51 | 7 | 1 | 1 | 2 | 0 | 2 | 48 | 0 | <1.00e-15 | <3.08e-14 | |
| 9 | HSA04650_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | Genes involved in natural killer cell mediated cytotoxicity | ARAF, BID, BRAF, CASP3, CD244, CD247, CD48, CHP, CSF2, FAS, FASLG, FCER1G, FCGR3A, FCGR3B, FYN, GRB2, GZMB, HCST, HLA-A, HLA-B, HLA-C, HLA-E, HLA-G, HRAS, ICAM1, ICAM2, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNG, IFNGR1, IFNGR2, ITGAL, ITGB2, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DS1, KIR2DS2, KIR3DL1, KIR3DL2, KLRC1, KLRC2, KLRC3, KLRD1, KLRK1, KRAS, LAT, LCK, LCP2, LOC652578, MAP2K1, MAP2K2, MAPK1, MAPK3, MICA, MICB, NCR1, NCR2, NCR3, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NRAS, PAK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRF1, PRKCA, PRKCB1, PRKCG, PTK2B, PTPN11, PTPN6, RAC1, RAC2, RAC3, RAF1, SH2D1A, SH2D1B, SH3BP2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SYK, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFSF10, TYROBP, ULBP1, ULBP2, ULBP3, VAV1, VAV2, VAV3, ZAP70 | 122 | CASP3(1), GZMB(1), HLA-B(2), IFNA16(1), ITGB2(1), KIR3DL1(3), KLRK1(1), KRAS(9), MAPK1(1), MICB(1), NFATC4(1), NRAS(18), PIK3CB(1), PIK3R2(1), PLCG2(1), PPP3CA(1), PRKCG(1), PTK2B(1), PTPN11(7), SHC1(1), SOS1(1), SYK(1), VAV3(1), ZAP70(1) | 31625279 | 58 | 48 | 41 | 9 | 6 | 23 | 4 | 24 | 1 | 0 | <1.00e-15 | <3.08e-14 |
| 10 | HSA04912_GNRH_SIGNALING_PATHWAY | Genes involved in GnRH signaling pathway | ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ATF4, CACNA1C, CACNA1D, CACNA1F, CACNA1S, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CDC42, CGA, EGFR, ELK1, FSHB, GNA11, GNAQ, GNAS, GNRH1, GNRH2, GNRHR, GRB2, HBEGF, HRAS, ITPR1, ITPR2, ITPR3, JUN, KRAS, LHB, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K6, MAP2K7, MAP3K1, MAP3K2, MAP3K3, MAP3K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK9, MMP14, MMP2, NRAS, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCB1, PLCB2, PLCB3, PLCB4, PLD1, PLD2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCD, PRKX, PRKY, PTK2B, RAF1, SOS1, SOS2, SRC | 91 | ADCY2(1), ADCY3(1), ADCY4(2), ADCY5(1), CACNA1D(1), CACNA1S(1), CDC42(1), EGFR(2), GNRHR(1), ITPR1(1), ITPR3(1), KRAS(9), MAP2K3(1), MAP3K4(4), MAPK1(1), NRAS(18), PLA2G2D(1), PLA2G3(1), PLCB3(1), PLD1(1), PTK2B(1), SOS1(1) | 36254019 | 52 | 47 | 34 | 7 | 7 | 20 | 3 | 19 | 3 | 0 | <1.00e-15 | <3.08e-14 |
Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10
| rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ERBB3PATHWAY | Neuregulins bind to the receptor tyrosine kinases ErbB3 and ErbB4, surface-localized receptors whose overexpression induces tumor formation. | EGF, EGFR, ERBB3, NRG1, UBE2D1 | 5 | EGF(1), EGFR(2), ERBB3(2), UBE2D1(1) | 2995149 | 6 | 6 | 6 | 1 | 1 | 1 | 0 | 3 | 1 | 0 | 0.00072 | 0.23 |
| 2 | HSA05130_PATHOGENIC_ESCHERICHIA_COLI_INFECTION_EHEC | Genes involved in pathogenic Escherichia coli infection - EHEC | ABL1, ACTB, ACTG1, ARHGEF2, ARPC5, ARPC5L, CD14, CDC42, CDH1, CLDN1, CTNNB1, CTTN, EZR, FYN, HCLS1, ITGB1, KRT18, LOC643224, LOC654264, LY96, NCK1, NCK2, NCL, OCLN, PRKCA, RHOA, ROCK1, ROCK2, TLR4, TLR5, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8, WAS, WASL, YWHAQ, YWHAZ | 51 | ABL1(2), CDC42(1), EZR(1), HCLS1(1), LY96(1), TLR4(1), TUBA1A(1), TUBA1B(1), TUBA3C(2), TUBB3(1), TUBB4(1), TUBB6(1), TUBB8(1), YWHAZ(1) | 15524189 | 16 | 16 | 16 | 6 | 4 | 3 | 2 | 6 | 1 | 0 | 0.0011 | 0.23 |
| 3 | HSA05131_PATHOGENIC_ESCHERICHIA_COLI_INFECTION_EPEC | Genes involved in pathogenic Escherichia coli infection - EPEC | ABL1, ACTB, ACTG1, ARHGEF2, ARPC5, ARPC5L, CD14, CDC42, CDH1, CLDN1, CTNNB1, CTTN, EZR, FYN, HCLS1, ITGB1, KRT18, LOC643224, LOC654264, LY96, NCK1, NCK2, NCL, OCLN, PRKCA, RHOA, ROCK1, ROCK2, TLR4, TLR5, TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA8, TUBAL3, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUBB8, WAS, WASL, YWHAQ, YWHAZ | 51 | ABL1(2), CDC42(1), EZR(1), HCLS1(1), LY96(1), TLR4(1), TUBA1A(1), TUBA1B(1), TUBA3C(2), TUBB3(1), TUBB4(1), TUBB6(1), TUBB8(1), YWHAZ(1) | 15524189 | 16 | 16 | 16 | 6 | 4 | 3 | 2 | 6 | 1 | 0 | 0.0011 | 0.23 |
| 4 | HSA04530_TIGHT_JUNCTION | Genes involved in tight junction | ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK | 123 | CDC42(1), CGN(1), CLDN11(1), CLDN16(1), CLDN18(1), CTNNA2(1), EXOC4(1), GNAI2(1), HCLS1(1), IGSF5(1), JAM2(1), LLGL2(1), MAGI1(1), MAGI2(1), MAGI3(1), MLLT4(2), MYH1(1), MYH13(2), MYH14(1), MYH15(1), MYH6(2), MYL9(1), PARD3(1), PPP2R1B(1), PPP2R2B(1), PPP2R3A(1), PRKCG(1), TJAP1(3), TJP1(1), TJP2(1) | 53804824 | 35 | 29 | 35 | 13 | 12 | 6 | 4 | 10 | 3 | 0 | 0.003 | 0.35 |
| 5 | GLUTATHIONE_METABOLISM | ANPEP, G6PD, GCLC, GCLM, GGT1, GPX1, GPX2, GPX3, GPX4, GPX5, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, PGD | 27 | G6PD(1), GCLM(1), GPX2(1), GSTM3(2), GSTT2(1), PGD(1) | 4736200 | 7 | 7 | 7 | 1 | 0 | 4 | 1 | 2 | 0 | 0 | 0.0033 | 0.35 | |
| 6 | HSA04810_REGULATION_OF_ACTIN_CYTOSKELETON | Genes involved in regulation of actin cytoskeleton | ABI2, ACTN1, ACTN2, ACTN3, ACTN4, APC, APC2, ARAF, ARHGEF1, ARHGEF12, ARHGEF4, ARHGEF6, ARHGEF7, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ARPC5L, BAIAP2, BCAR1, BDKRB1, BDKRB2, BRAF, C3orf10, CD14, CDC42, CFL1, CFL2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CRK, CRKL, CSK, CYFIP1, CYFIP2, DIAPH1, DIAPH2, DIAPH3, DOCK1, EGF, EGFR, EZR, F2, F2R, FGD1, FGD3, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FN1, GIT1, GNA12, GNA13, GNG12, GRLF1, GSN, HRAS, INS, IQGAP1, IQGAP2, IQGAP3, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAD, ITGAE, ITGAL, ITGAM, ITGAV, ITGAX, ITGB1, ITGB2, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, KRAS, LIMK1, LIMK2, LOC200025, LOC645126, LOC653888, MAP2K1, MAP2K2, MAPK1, MAPK3, MLCK, MOS, MRAS, MRCL3, MRLC2, MSN, MYH10, MYH14, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, NCKAP1, NCKAP1L, NRAS, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDGFA, PDGFB, PDGFRA, PDGFRB, PFN1, PFN2, PFN3, PFN4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PPP1R12B, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RDX, RHOA, ROCK1, ROCK2, RRAS, RRAS2, SCIN, SLC9A1, SOS1, SOS2, SSH1, SSH2, SSH3, TIAM1, TIAM2, TMSB4X, TMSB4Y, TMSL3, VAV1, VAV2, VAV3, VCL, WAS, WASF1, WASF2, WASL | 191 | APC(4), ARHGEF1(1), ARHGEF6(1), BAIAP2(1), CDC42(1), DIAPH2(1), DOCK1(1), EGF(1), EGFR(2), EZR(1), FGF8(1), FN1(2), IQGAP3(3), ITGA10(1), ITGA11(1), ITGA4(1), ITGAD(2), ITGAV(1), ITGAX(1), ITGB2(1), MAPK1(1), MYH14(1), MYL9(1), MYLK(1), MYLK2(1), PDGFRA(1), PDGFRB(1), PIK3CB(1), PIK3R2(1), PIP5K1B(1), PIP5K1C(1), PPP1R12A(1), SOS1(1), SSH3(1), TIAM2(1), TMSL3(1), VAV3(1) | 77184737 | 45 | 33 | 45 | 10 | 13 | 9 | 6 | 13 | 4 | 0 | 0.0034 | 0.35 |
| 7 | CIRCADIAN_EXERCISE | ARNTL, AZIN1, BTG1, C10orf110, C1orf1, CBX3, CEBPB, CLDN5, CLOCK, CRY1, CRY2, DAZAP2, DAZAP2, LOC401029, DNAJA1, EIF4G2, ETV6, G0S2, GENX_3414, GFRA1, GSTM3, GSTP1, HERPUD1, HLA_DMA, HSPA8, IDI1, KLF9, MAP3K7IP2, MYF6, NCKAP1, NCOA4, NR1D2, OAZIN, PER1, PER2, PIGF, PPP1R3C, PPP2CB, PSMA4, PURA, SF3A3, SUMO3, TOB1, TUBB3, UCP3, UGP2, VAPA, ZFR | 36 | CRY1(1), DAZAP2(1), GSTM3(2), NR1D2(1), PIGF(1), PURA(1), TUBB3(1) | 10039948 | 8 | 8 | 8 | 2 | 0 | 0 | 3 | 3 | 2 | 0 | 0.0059 | 0.52 | |
| 8 | HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION | Genes involved in neuroactive ligand-receptor interaction | ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2 | 220 | ADRA1A(1), BRS3(1), C5AR1(1), CRHR2(1), CTSG(1), DRD2(1), F2RL1(1), GABBR1(1), GABRA4(1), GABRB1(1), GABRG2(1), GABRR1(1), GHR(1), GLRA1(1), GNRHR(1), GPR156(1), GPR50(1), GRID1(2), GRIK2(3), GRIK3(2), GRIK4(3), GRIK5(1), GRIN3A(1), GRM3(2), GRM5(1), GRM6(2), GRM8(2), HTR5A(1), MCHR2(1), NMUR2(3), NTSR2(1), OPRM1(1), P2RX7(1), P2RY1(1), P2RY2(2), PARD3(1), PRSS3(1), SCTR(1), SSTR4(1), THRA(1), THRB(1), VIPR1(2) | 60973003 | 55 | 41 | 55 | 16 | 18 | 18 | 3 | 13 | 3 | 0 | 0.0068 | 0.53 |
| 9 | HSA00480_GLUTATHIONE_METABOLISM | Genes involved in glutathione metabolism | ANPEP, G6PD, GCLC, GCLM, GGT1, GGTL3, GGTL4, GPX1, GPX2, GPX3, GPX4, GPX5, GPX6, GPX7, GSR, GSS, GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTK1, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO2, GSTP1, GSTT1, GSTT2, GSTZ1, IDH1, IDH2, MGST1, MGST2, MGST3, OPLAH, TXNDC12 | 31 | G6PD(1), GCLM(1), GPX2(1), GSTM3(2), GSTT2(1) | 5168229 | 6 | 6 | 6 | 1 | 0 | 3 | 1 | 2 | 0 | 0 | 0.0095 | 0.63 |
| 10 | HSA04020_CALCIUM_SIGNALING_PATHWAY | Genes involved in calcium signaling pathway | ADCY1, ADCY2, ADCY3, ADCY4, ADCY7, ADCY8, ADCY9, ADORA2A, ADORA2B, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, AGTR1, ATP2A1, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, ATP2B4, AVPR1A, AVPR1B, BDKRB1, BDKRB2, BST1, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CCKAR, CCKBR, CD38, CHP, CHRM1, CHRM2, CHRM3, CHRM5, CHRNA7, CYSLTR1, CYSLTR2, DRD1, EDNRA, EDNRB, EGFR, ERBB2, ERBB3, ERBB4, F2R, GNA11, GNA14, GNA15, GNAL, GNAQ, GNAS, GRIN1, GRIN2A, GRIN2C, GRIN2D, GRM1, GRM5, GRPR, HRH1, HRH2, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, LHCGR, LTB4R2, MLCK, MYLK, MYLK2, NOS1, NOS2A, NOS3, NTSR1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, PDE1A, PDE1B, PDE1C, PDGFRA, PDGFRB, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PLN, PPID, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTAFR, PTGER1, PTGER3, PTGFR, PTK2B, RYR1, RYR2, RYR3, SLC25A4, SLC25A5, SLC25A6, SLC8A1, SLC8A2, SLC8A3, SPHK1, SPHK2, TACR1, TACR2, TACR3, TBXA2R, TNNC1, TNNC2, TRHR, TRPC1, VDAC1, VDAC2, VDAC3 | 163 | ADCY2(1), ADCY3(1), ADCY4(2), ADRA1A(1), ATP2A2(1), ATP2B2(1), ATP2B3(1), CACNA1B(3), CACNA1D(1), CACNA1E(3), CACNA1G(2), CACNA1I(1), CACNA1S(1), CAMK4(1), EGFR(2), ERBB3(2), GNA15(1), GRM5(1), HTR5A(1), ITPR1(1), ITPR3(1), MYLK(1), MYLK2(1), NOS1(1), P2RX7(1), PDGFRA(1), PDGFRB(1), PHKG1(1), PLCB3(1), PLCD4(1), PLCE1(4), PLCG2(1), PLCZ1(1), PPP3CA(1), PRKCG(1), PTK2B(1), RYR1(1), RYR3(4), TNNC2(1), TRPC1(1), VDAC1(1) | 76549927 | 55 | 39 | 55 | 21 | 14 | 12 | 7 | 20 | 2 | 0 | 0.012 | 0.63 |
+
Methods & Data
+
Methods
In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset. [1]
+
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
+
References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 - 615 (2011)
Copyright © 2012
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.