(metastatic tumor cohort)
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.
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Working with individual set: SKCM-TM
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Number of patients in set: 225
The input for this pipeline is a set of individuals with the following files associated for each:
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An annotated .maf file describing the mutations called for the respective individual, and their properties.
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A .wig file that contains information about the coverage of the sample.
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MAF used for this analysis:SKCM-TM.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 94
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Mutations seen in COSMIC: 595
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Significantly mutated genes in COSMIC territory: 41
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Genes with clustered mutations (≤ 3 aa apart): 1204
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Significantly mutated genesets: 2
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Significantly mutated genesets: (excluding sig. mutated genes):0
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Read 225 MAFs of type "Broad"
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Total number of mutations in input MAFs: 172938
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After removing 4 mutations outside chr1-24: 172934
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After removing 790 blacklisted mutations: 172144
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After removing 3204 noncoding mutations: 168940
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After collapsing adjacent/redundant mutations: 168893
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Number of mutations before filtering: 168893
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After removing 2144 mutations outside gene set: 166749
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After removing 109 mutations outside category set: 166640
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After removing 7 "impossible" mutations in
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gene-patient-category bins of zero coverage: 164380
Table 1. Get Full Table Table representing breakdown of mutations by type.
| type | count |
|---|---|
| Frame_Shift_Del | 907 |
| Frame_Shift_Ins | 263 |
| In_Frame_Del | 335 |
| In_Frame_Ins | 49 |
| Missense_Mutation | 102016 |
| Nonsense_Mutation | 6387 |
| Nonstop_Mutation | 44 |
| Silent | 54905 |
| Splice_Site | 1686 |
| Translation_Start_Site | 48 |
| Total | 166640 |
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 | exp_ns_s_ratio |
|---|---|---|---|---|---|---|
| (C/T)p*C->T | 75380 | 1788133353 | 0.000042 | 42 | 2.4 | 1.6 |
| (A/G)p*C->T | 8507 | 1500436990 | 5.7e-06 | 5.7 | 0.33 | 1.9 |
| A->G | 4901 | 3176808123 | 1.5e-06 | 1.5 | 0.089 | 2.3 |
| transver | 13227 | 6465378466 | 2e-06 | 2 | 0.12 | 5 |
| indel+null | 9614 | 6465378466 | 1.5e-06 | 1.5 | 0.086 | NaN |
| double_null | 102 | 6465378466 | 1.6e-08 | 0.016 | 0.00091 | NaN |
| Total | 111731 | 6465378466 | 0.000017 | 17 | 1 | 3.5 |
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.
Figure 2. Patients counts and rates file used to generate this plot: SKCM-TM.patients.counts_and_rates.txt
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.
Column Descriptions:
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N = number of sequenced bases in this gene across the individual set
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n = number of (nonsilent) mutations in this gene across the individual set
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npat = number of patients (individuals) with at least one nonsilent mutation
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nsite = number of unique sites having a non-silent mutation
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nsil = number of silent mutations in this gene across the individual set
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n1 = number of nonsilent mutations of type: (C/T)p*C->T
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n2 = number of nonsilent mutations of type: (A/G)p*C->T
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n3 = number of nonsilent mutations of type: A->G
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n4 = number of nonsilent mutations of type: transver
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n5 = number of nonsilent mutations of type: indel+null
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n6 = number of nonsilent mutations of type: double_null
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p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
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p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
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p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene
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p_joint = p-value for clustering + conservation
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p = p-value (overall)
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q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 94. 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_ns_s | p_cons | p_joint | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 498822 | 120 | 115 | 16 | 2 | 11 | 1 | 5 | 103 | 0 | 0 | <1.00e-15 | 2.3e-09 | NaN | NaN | <1.00e-15 | <9.03e-12 |
| 2 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 131798 | 65 | 65 | 9 | 1 | 2 | 1 | 22 | 40 | 0 | 0 | <1.00e-15 | 1.4e-06 | NaN | NaN | <1.00e-15 | <9.03e-12 |
| 3 | CDKN2A | cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) | 206066 | 31 | 31 | 15 | 1 | 9 | 0 | 0 | 1 | 21 | 0 | 3.33e-15 | 0.00083 | NaN | NaN | 3.33e-15 | 1.95e-11 |
| 4 | TP53 | tumor protein p53 | 272813 | 37 | 34 | 31 | 1 | 15 | 0 | 4 | 4 | 14 | 0 | 4.33e-15 | 0.000028 | NaN | NaN | 4.33e-15 | 1.95e-11 |
| 5 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 254423 | 18 | 18 | 16 | 0 | 1 | 0 | 3 | 3 | 11 | 0 | 8.49e-14 | 0.046 | NaN | NaN | 8.49e-14 | 3.07e-10 |
| 6 | ACSM2B | acyl-CoA synthetase medium-chain family member 2B | 390509 | 42 | 36 | 32 | 5 | 34 | 2 | 0 | 2 | 4 | 0 | 5.96e-10 | 0.000053 | NaN | NaN | 5.96e-10 | 1.79e-06 |
| 7 | LCE1B | late cornified envelope 1B | 81085 | 13 | 13 | 13 | 0 | 8 | 0 | 0 | 3 | 2 | 0 | 1.34e-09 | 0.042 | NaN | NaN | 1.34e-09 | 3.45e-06 |
| 8 | CADM2 | cell adhesion molecule 2 | 289047 | 28 | 22 | 26 | 3 | 18 | 9 | 0 | 1 | 0 | 0 | 1.88e-08 | 0.0067 | NaN | NaN | 1.88e-08 | 4.24e-05 |
| 9 | RAC1 | ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) | 138204 | 16 | 16 | 8 | 1 | 14 | 0 | 0 | 2 | 0 | 0 | 5.04e-08 | 0.004 | NaN | NaN | 5.04e-08 | 9.95e-05 |
| 10 | NAP1L2 | nucleosome assembly protein 1-like 2 | 307024 | 23 | 21 | 22 | 1 | 16 | 1 | 2 | 2 | 2 | 0 | 5.51e-08 | 0.003 | NaN | NaN | 5.51e-08 | 9.95e-05 |
| 11 | MUC7 | mucin 7, secreted | 255653 | 22 | 19 | 17 | 1 | 14 | 1 | 6 | 0 | 1 | 0 | 1.17e-07 | 0.0013 | NaN | NaN | 1.17e-07 | 0.000192 |
| 12 | OR51S1 | olfactory receptor, family 51, subfamily S, member 1 | 218336 | 27 | 26 | 18 | 6 | 21 | 3 | 0 | 1 | 2 | 0 | 1.70e-07 | 0.0023 | NaN | NaN | 1.70e-07 | 0.000255 |
| 13 | USP29 | ubiquitin specific peptidase 29 | 623157 | 43 | 35 | 38 | 4 | 31 | 1 | 4 | 2 | 5 | 0 | 2.14e-07 | 0.000071 | NaN | NaN | 2.14e-07 | 0.000283 |
| 14 | FUT9 | fucosyltransferase 9 (alpha (1,3) fucosyltransferase) | 224540 | 22 | 22 | 21 | 4 | 15 | 2 | 1 | 4 | 0 | 0 | 2.25e-07 | 0.058 | NaN | NaN | 2.25e-07 | 0.000283 |
| 15 | PPP6C | protein phosphatase 6, catalytic subunit | 225775 | 18 | 17 | 13 | 2 | 12 | 0 | 0 | 2 | 4 | 0 | 2.35e-07 | 0.078 | NaN | NaN | 2.35e-07 | 0.000283 |
| 16 | RPTN | repetin | 531666 | 47 | 38 | 42 | 4 | 35 | 2 | 4 | 6 | 0 | 0 | 3.01e-07 | 0.0015 | NaN | NaN | 3.01e-07 | 0.000340 |
| 17 | TAF1A | TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa | 313386 | 14 | 14 | 7 | 0 | 1 | 0 | 0 | 13 | 0 | 0 | 5.54e-07 | 0.13 | NaN | NaN | 5.54e-07 | 0.000589 |
| 18 | ZNF679 | zinc finger protein 679 | 176141 | 19 | 18 | 15 | 2 | 15 | 0 | 1 | 3 | 0 | 0 | 7.24e-07 | 0.032 | NaN | NaN | 7.24e-07 | 0.000709 |
| 19 | GRXCR1 | glutaredoxin, cysteine rich 1 | 195954 | 20 | 18 | 18 | 3 | 11 | 2 | 2 | 1 | 4 | 0 | 7.88e-07 | 0.04 | NaN | NaN | 7.88e-07 | 0.000709 |
| 20 | CDH9 | cadherin 9, type 2 (T1-cadherin) | 525372 | 37 | 32 | 34 | 4 | 30 | 1 | 0 | 3 | 3 | 0 | 8.11e-07 | 0.0061 | NaN | NaN | 8.11e-07 | 0.000709 |
| 21 | HIST1H2AA | histone cluster 1, H2aa | 89998 | 10 | 10 | 8 | 0 | 5 | 1 | 0 | 3 | 1 | 0 | 8.24e-07 | 0.037 | NaN | NaN | 8.24e-07 | 0.000709 |
| 22 | C8A | complement component 8, alpha polypeptide | 384948 | 29 | 26 | 25 | 2 | 24 | 1 | 0 | 1 | 3 | 0 | 1.39e-06 | 0.00048 | NaN | NaN | 1.39e-06 | 0.00114 |
| 23 | RBM11 | RNA binding motif protein 11 | 146951 | 12 | 12 | 10 | 0 | 7 | 0 | 0 | 2 | 3 | 0 | 1.66e-06 | 0.086 | NaN | NaN | 1.66e-06 | 0.00130 |
| 24 | ZNF479 | zinc finger protein 479 | 338455 | 23 | 22 | 18 | 3 | 16 | 0 | 1 | 5 | 1 | 0 | 2.35e-06 | 0.051 | NaN | NaN | 2.35e-06 | 0.00176 |
| 25 | GFRAL | GDNF family receptor alpha like | 268883 | 32 | 28 | 30 | 8 | 25 | 2 | 0 | 2 | 3 | 0 | 3.57e-06 | 0.089 | NaN | NaN | 3.57e-06 | 0.00258 |
| 26 | DDX3X | DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked | 442121 | 18 | 18 | 17 | 0 | 6 | 1 | 2 | 2 | 7 | 0 | 4.08e-06 | 0.019 | NaN | NaN | 4.08e-06 | 0.00283 |
| 27 | OR4M2 | olfactory receptor, family 4, subfamily M, member 2 | 210657 | 28 | 22 | 21 | 8 | 20 | 3 | 1 | 3 | 1 | 0 | 5.03e-06 | 0.0026 | NaN | NaN | 5.03e-06 | 0.00336 |
| 28 | FRG2B | FSHD region gene 2 family, member B | 117951 | 17 | 17 | 11 | 4 | 13 | 1 | 1 | 2 | 0 | 0 | 5.28e-06 | 0.092 | NaN | NaN | 5.28e-06 | 0.00341 |
| 29 | PDE1A | phosphodiesterase 1A, calmodulin-dependent | 380523 | 32 | 30 | 27 | 5 | 25 | 1 | 0 | 5 | 1 | 0 | 8.27e-06 | 0.018 | NaN | NaN | 8.27e-06 | 0.00515 |
| 30 | PRB2 | proline-rich protein BstNI subfamily 2 | 280074 | 37 | 29 | 35 | 2 | 33 | 1 | 1 | 1 | 1 | 0 | 9.99e-06 | 0.07 | NaN | NaN | 9.99e-06 | 0.00601 |
| 31 | LUZP2 | leucine zipper protein 2 | 222460 | 20 | 19 | 17 | 4 | 16 | 0 | 1 | 2 | 1 | 0 | 1.15e-05 | 0.094 | NaN | NaN | 1.15e-05 | 0.00663 |
| 32 | NRK | Nik related kinase | 548842 | 29 | 28 | 28 | 4 | 22 | 0 | 0 | 3 | 4 | 0 | 1.17e-05 | 0.017 | NaN | NaN | 1.17e-05 | 0.00663 |
| 33 | PARM1 | prostate androgen-regulated mucin-like protein 1 | 199712 | 17 | 17 | 15 | 2 | 13 | 2 | 0 | 1 | 1 | 0 | 1.44e-05 | 0.025 | NaN | NaN | 1.44e-05 | 0.00775 |
| 34 | SLC38A4 | solute carrier family 38, member 4 | 345882 | 27 | 25 | 21 | 4 | 22 | 1 | 1 | 3 | 0 | 0 | 1.46e-05 | 0.0096 | NaN | NaN | 1.46e-05 | 0.00775 |
| 35 | PRAMEF11 | PRAME family member 11 | 279205 | 24 | 21 | 19 | 7 | 8 | 2 | 4 | 6 | 4 | 0 | 1.73e-05 | 0.067 | NaN | NaN | 1.73e-05 | 0.00873 |
Figure S1. This figure depicts the distribution of mutations and mutation types across the BRAF significant gene.
Figure S2. This figure depicts the distribution of mutations and mutation types across the NRAS significant gene.
Figure S3. This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.
Figure S4. This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.
Figure S5. This figure depicts the distribution of mutations and mutation types across the PTEN significant gene.
Figure S6. This figure depicts the distribution of mutations and mutation types across the ACSM2B significant gene.
Figure S7. This figure depicts the distribution of mutations and mutation types across the LCE1B significant gene.
Figure S8. This figure depicts the distribution of mutations and mutation types across the CADM2 significant gene.
Figure S9. This figure depicts the distribution of mutations and mutation types across the RAC1 significant gene.
Figure S10. This figure depicts the distribution of mutations and mutation types across the NAP1L2 significant gene.
Figure S11. This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.
Figure S12. This figure depicts the distribution of mutations and mutation types across the OR51S1 significant gene.
Figure S13. This figure depicts the distribution of mutations and mutation types across the USP29 significant gene.
Figure S14. This figure depicts the distribution of mutations and mutation types across the FUT9 significant gene.
Figure S15. This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.
Figure S16. This figure depicts the distribution of mutations and mutation types across the RPTN significant gene.
Figure S17. This figure depicts the distribution of mutations and mutation types across the TAF1A significant gene.
Figure S18. This figure depicts the distribution of mutations and mutation types across the ZNF679 significant gene.
Figure S19. This figure depicts the distribution of mutations and mutation types across the GRXCR1 significant gene.
Figure S20. This figure depicts the distribution of mutations and mutation types across the CDH9 significant gene.
Figure S21. This figure depicts the distribution of mutations and mutation types across the HIST1H2AA significant gene.
Figure S22. This figure depicts the distribution of mutations and mutation types across the C8A significant gene.
Figure S23. This figure depicts the distribution of mutations and mutation types across the RBM11 significant gene.
Figure S24. This figure depicts the distribution of mutations and mutation types across the ZNF479 significant gene.
Figure S25. This figure depicts the distribution of mutations and mutation types across the GFRAL significant gene.
Figure S26. This figure depicts the distribution of mutations and mutation types across the DDX3X significant gene.
Figure S27. This figure depicts the distribution of mutations and mutation types across the OR4M2 significant gene.
Figure S28. This figure depicts the distribution of mutations and mutation types across the FRG2B significant gene.
Figure S29. This figure depicts the distribution of mutations and mutation types across the PDE1A significant gene.
Figure S30. This figure depicts the distribution of mutations and mutation types across the LUZP2 significant gene.
Figure S31. This figure depicts the distribution of mutations and mutation types across the NRK significant gene.
Figure S32. This figure depicts the distribution of mutations and mutation types across the PARM1 significant gene.
Figure S33. This figure depicts the distribution of mutations and mutation types across the SLC38A4 significant gene.
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: 41. Number of genes displayed: 10
| rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q |
|---|---|---|---|---|---|---|---|---|---|
| 1 | STK19 | serine/threonine kinase 19 | 12 | 2 | 6 | 450 | 12 | 0 | 0 |
| 2 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 65 | 33 | 63 | 7425 | 78387 | 0 | 0 |
| 3 | IDH1 | isocitrate dehydrogenase 1 (NADP+), soluble | 11 | 5 | 9 | 1125 | 13428 | 0 | 0 |
| 4 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 120 | 89 | 114 | 20025 | 1479650 | 0 | 0 |
| 5 | TP53 | tumor protein p53 | 37 | 356 | 35 | 80100 | 3367 | 0 | 0 |
| 6 | CDKN2A | cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) | 31 | 332 | 31 | 74700 | 1172 | 0 | 0 |
| 7 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 18 | 767 | 18 | 172575 | 374 | 3.3e-09 | 2.1e-06 |
| 8 | EPHA6 | EPH receptor A6 | 58 | 8 | 4 | 1800 | 4 | 3.8e-08 | 0.000021 |
| 9 | EPHA7 | EPH receptor A7 | 36 | 13 | 4 | 2925 | 4 | 2.6e-07 | 0.00011 |
| 10 | RIPK4 | receptor-interacting serine-threonine kinase 4 | 8 | 3 | 3 | 675 | 3 | 2.6e-07 | 0.00011 |
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)
Table 5. Get Full Table Genes with Clustered Mutations
| num | gene | desc | n | mindist | nmuts0 | nmuts3 | nmuts12 | npairs0 | npairs3 | npairs12 |
|---|---|---|---|---|---|---|---|---|---|---|
| 1330 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 120 | 0 | 3582 | 4024 | 4117 | 3582 | 4024 | 4117 |
| 9126 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 65 | 0 | 1491 | 1495 | 1501 | 1491 | 1495 | 1501 |
| 8549 | MUC16 | mucin 16, cell surface associated | 665 | 0 | 95 | 184 | 469 | 95 | 184 | 469 |
| 14404 | TTN | titin | 914 | 0 | 74 | 113 | 275 | 74 | 113 | 275 |
| 3917 | DNAH5 | dynein, axonemal, heavy chain 5 | 274 | 0 | 74 | 105 | 254 | 74 | 105 | 254 |
| 9980 | PCLO | piccolo (presynaptic cytomatrix protein) | 240 | 0 | 53 | 93 | 194 | 53 | 93 | 194 |
| 11166 | RAC1 | ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) | 16 | 0 | 45 | 45 | 56 | 45 | 45 | 56 |
| 6375 | IDH1 | isocitrate dehydrogenase 1 (NADP+), soluble | 11 | 0 | 36 | 36 | 36 | 36 | 36 | 36 |
| 3083 | CNTN5 | contactin 5 | 65 | 0 | 32 | 42 | 69 | 32 | 42 | 69 |
| 13685 | THSD7B | thrombospondin, type I, domain containing 7B | 111 | 0 | 31 | 62 | 129 | 31 | 62 | 129 |
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.
Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 2. 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_ns_s | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ST_G_ALPHA_S_PATHWAY | The G-alpha-s protein activates adenylyl cyclases, which catalyze cAMP formation. | ASAH1, BF, BFAR, BRAF, CAMP, CREB1, CREB3, CREB5, EPAC, GAS, GRF2, MAPK1, RAF1, SNX13, SRC, TERF2IP | 12 | BRAF(120), CAMP(1), CREB3(1), CREB5(7), MAPK1(4), RAF1(7), SNX13(1), SRC(1), TERF2IP(1) | 3702957 | 143 | 127 | 39 | 25 | 24 | 4 | 6 | 106 | 3 | 0 | 0.0069 | 6.9e-15 | 4.2e-12 |
| 2 | SA_G1_AND_S_PHASES | Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. | ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53 | 15 | CCND1(1), CDK4(5), CDKN1A(4), CDKN1B(1), CDKN2A(31), CFL1(1), E2F1(4), E2F2(4), MDM2(3), NXT1(1), PRB1(26), TP53(37) | 2797685 | 118 | 78 | 92 | 14 | 54 | 3 | 6 | 16 | 39 | 0 | 6e-09 | 9.1e-07 | 0.00028 |
| 3 | SA_REG_CASCADE_OF_CYCLIN_EXPR | Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. | CCNA1, CCNA2, CCND1, CCNE1, CCNE2, CDK2, CDK4, CDKN1B, CDKN2A, E2F1, E2F2, E2F4, PRB1 | 13 | CCNA1(13), CCND1(1), CCNE1(3), CCNE2(12), CDK4(5), CDKN1B(1), CDKN2A(31), E2F1(4), E2F2(4), E2F4(1), PRB1(26) | 2981654 | 101 | 74 | 77 | 14 | 55 | 0 | 4 | 18 | 24 | 0 | 1.5e-06 | 0.0094 | 1 |
| 4 | HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM | Genes involved in D-arginine and D-ornithine metabolism | DAO | 1 | DAO(9) | 237556 | 9 | 9 | 9 | 1 | 6 | 1 | 1 | 1 | 0 | 0 | 0.073 | 0.04 | 1 |
| 5 | TERTPATHWAY | hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers. | HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42 | 7 | HDAC1(1), MYC(4), SP1(3), TP53(37), WT1(4) | 2347608 | 49 | 41 | 43 | 7 | 22 | 1 | 7 | 5 | 14 | 0 | 0.0016 | 0.23 | 1 |
| 6 | ARFPATHWAY | Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest. | ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1 | 16 | ABL1(10), CDKN2A(31), E2F1(4), MDM2(3), MYC(4), PIK3CA(6), PIK3R1(3), POLR1A(11), POLR1B(8), RAC1(16), RB1(8), TBX2(6), TP53(37), TWIST1(1) | 6692195 | 148 | 92 | 118 | 20 | 74 | 7 | 6 | 16 | 42 | 3 | 8.5e-10 | 0.25 | 1 |
| 7 | HSA00627_1,4_DICHLOROBENZENE_DEGRADATION | Genes involved in 1,4-dichlorobenzene degradation | CMBL | 1 | CMBL(3) | 170466 | 3 | 3 | 3 | 1 | 3 | 0 | 0 | 0 | 0 | 0 | 0.61 | 0.49 | 1 |
| 8 | HSA00401_NOVOBIOCIN_BIOSYNTHESIS | Genes involved in novobiocin biosynthesis | GOT1, GOT2, TAT | 3 | GOT1(3), GOT2(4), TAT(12) | 871759 | 19 | 16 | 18 | 4 | 12 | 2 | 2 | 1 | 2 | 0 | 0.033 | 0.53 | 1 |
| 9 | SLRPPATHWAY | Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. | BGN, DCN, DSPG3, FMOD, KERA, LUM | 5 | BGN(5), DCN(15), FMOD(4), KERA(13), LUM(10) | 1162061 | 47 | 37 | 44 | 14 | 36 | 4 | 3 | 1 | 3 | 0 | 0.0024 | 0.66 | 1 |
| 10 | FOSBPATHWAY | FOSB gene expression and drug abuse | CDK5, FOSB, GRIA2, JUND, PPP1R1B | 5 | CDK5(4), FOSB(5), GRIA2(31), JUND(1), PPP1R1B(2) | 1208725 | 43 | 38 | 40 | 14 | 26 | 3 | 2 | 5 | 7 | 0 | 0.076 | 0.68 | 1 |
Table 7. 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_ns_s | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM | Genes involved in D-arginine and D-ornithine metabolism | DAO | 1 | DAO(9) | 237556 | 9 | 9 | 9 | 1 | 6 | 1 | 1 | 1 | 0 | 0 | 0.073 | 0.04 | 1 |
| 2 | HSA00627_1,4_DICHLOROBENZENE_DEGRADATION | Genes involved in 1,4-dichlorobenzene degradation | CMBL | 1 | CMBL(3) | 170466 | 3 | 3 | 3 | 1 | 3 | 0 | 0 | 0 | 0 | 0 | 0.61 | 0.49 | 1 |
| 3 | HSA00401_NOVOBIOCIN_BIOSYNTHESIS | Genes involved in novobiocin biosynthesis | GOT1, GOT2, TAT | 3 | GOT1(3), GOT2(4), TAT(12) | 871759 | 19 | 16 | 18 | 4 | 12 | 2 | 2 | 1 | 2 | 0 | 0.033 | 0.53 | 1 |
| 4 | SLRPPATHWAY | Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. | BGN, DCN, DSPG3, FMOD, KERA, LUM | 5 | BGN(5), DCN(15), FMOD(4), KERA(13), LUM(10) | 1162061 | 47 | 37 | 44 | 14 | 36 | 4 | 3 | 1 | 3 | 0 | 0.0024 | 0.66 | 1 |
| 5 | FOSBPATHWAY | FOSB gene expression and drug abuse | CDK5, FOSB, GRIA2, JUND, PPP1R1B | 5 | CDK5(4), FOSB(5), GRIA2(31), JUND(1), PPP1R1B(2) | 1208725 | 43 | 38 | 40 | 14 | 26 | 3 | 2 | 5 | 7 | 0 | 0.076 | 0.68 | 1 |
| 6 | BOTULINPATHWAY | Blockade of Neurotransmitter Relase by Botulinum Toxin | CHRM1, CHRNA1, SNAP25, STX1A, VAMP2 | 5 | CHRM1(3), CHRNA1(5), SNAP25(5), STX1A(2) | 1083206 | 15 | 14 | 13 | 2 | 9 | 1 | 0 | 1 | 4 | 0 | 0.013 | 0.89 | 1 |
| 7 | BBCELLPATHWAY | Fas ligand expression by T cells induces apoptosis in Fas-expressing, inactive B cells. | CD28, CD4, HLA-DRA, HLA-DRB1, TNFRSF5, TNFRSF6, TNFSF5, TNFSF6 | 4 | CD28(1), CD4(6), HLA-DRA(10), HLA-DRB1(3) | 777496 | 20 | 18 | 20 | 8 | 15 | 1 | 0 | 3 | 1 | 0 | 0.14 | 0.96 | 1 |
| 8 | INOSITOL_METABOLISM | ALDH6A1, ALDOA, ALDOB, ALDOC, TPI1 | 5 | ALDH6A1(3), ALDOA(1), ALDOB(9), ALDOC(3) | 1307091 | 16 | 14 | 13 | 4 | 11 | 2 | 0 | 1 | 2 | 0 | 0.061 | 0.96 | 1 | |
| 9 | HSA00785_LIPOIC_ACID_METABOLISM | Genes involved in lipoic acid metabolism | LIAS, LIPT1, LOC387787 | 2 | LIPT1(2) | 512888 | 2 | 2 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0.63 | 0.97 | 1 |
| 10 | PEPIPATHWAY | Proepithelin (PEPI) induces epithelial cells to secrete IL-8, which promotes elastase secretion by neutrophils. | ELA1, ELA2, ELA2A, ELA2B, ELA3B, GRN, IL8, SLPI | 3 | GRN(3), IL8(1), SLPI(5) | 569288 | 9 | 9 | 9 | 4 | 4 | 1 | 0 | 4 | 0 | 0 | 0.62 | 0.97 | 1 |
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]
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.