| Name |
Description |
Default Score |
Score Details (if any) |
Number of genes |
| BACKGROUND: Broad 2000 Cancer Gene List |
Genes on the Broad list of cancer targets with hybrid capture assays designed. Various sources. Sent by Carrie Sougnez of the Broad Institute. |
1.000 |
-- |
1871 |
| BACKGROUND: COSMIC human mutated genes, >= 2% of all samples |
Genes obtained from [COSMIC] and known to show mutations in human tissue in 2 or more percent of sequenced samples. |
1.000 |
-- |
350 |
| BACKGROUND: Genes in fragile sites |
Genes in fragile sites FRA16D, FRA6E, FRA9E, originally nominated by the NCI ovarian caner genes list. |
1.000 |
-- |
31 |
| BACKGROUND: NCI Cancer Genes - lung |
NCI curated lung cancer genes, exctracted from the literature. Submitted by Carl Schaefer, NCI. |
.250 |
-- |
1103 |
| BACKGROUND: NCI Cancer Genes - ovarian |
NCI curated ovarian cancer genes, exctracted from the literature. Submitted by Carl Schaefer, NCI. |
1.000 |
-- |
808 |
| BACKGROUND: Ovarian cancer candidate genes |
Genes nominated by the ovarian WG. Submitted by Joe Gray. |
1.000 |
-- |
503 |
| BACKGROUND: Review Paper by Hahn and Weinberg |
Hahn WC, Weinberg RA., Modelling the molecular circuitry of cancer. Nat Rev Cancer. 2002 May;2(5):331-41. [PubMed]. Gene list derived from MSKCC CancerGenes Resource. |
1.000 |
-- |
41 |
| BACKGROUND: Review Paper by Volgestein and Kinzler |
Vogelstein B, Kinzler KW., Cancer genes and the pathways they control. Nat Med. 2004 Aug;10(8):789-99. [PubMed]. Gene list derived from MSKCC CancerGenes Resource. |
1.000 |
-- |
112 |
| BACKGROUND: Sanger Gene Census |
Sanger Cancer Gene Census, [Census Details] The Cancer Gene Census is an ongoing effort to catalogue those genes for which mutations have been causally implicated in cancer. The original census and analysis was published in Nature Reviews Cancer and supplemental analysis information related to the paper is also available." |
1.000 |
-- |
379 |
| PATHWAYS: Cancer-associated pathways, 1 mutation |
Contains a list of candidate gene culled from cancer-associated pathway databases that showed exactly one mutation in the three Vogelstein cancer genomics papers. Pathway involvement is indicated in the comment field. Submitted by Lawrence A. Donehower and David Wheeler, Baylor College of Medicine. |
1.000 |
-- |
207 |
| PATHWAYS: Cancer-associated pathways, >=2 mutations |
Contains a list of candidate gene culled from cancer-associated pathway databases that showed at least two mutation in the three Vogelstein cancer genomics papers. Pathway involvement is indicated in the comment field. Submitted by Lawrence A. Donehower and David Wheeler, Baylor College of Medicine. |
1.000 |
-- |
80 |
| PATHWAYS: Expert lists |
Genes merged from various expert lists. |
1.000 |
-- |
255 |
| PATHWAYS: Extension of core GBM pathways |
Pathway extension was performed with the 8 significantly mutated genes in TCGA GBM used as seeds: TP53 PTEN NF1 EGFR ERBB2 RB1 PIK3R1 PIK3CA. These eight genes form the core pathways defined in the first TCGA paper. Four iterations of network extension were performed. At each iteration, altered gene neighbors were added to the core pathway. Alteration is determined by sequence mutation, high-level amplification or homozygous deletion in >2% of all cases. All genes in this network are therefore implicated by a combination of factors including: network topology, frequency of sequence mutation and frequency of CNA alteration. Network data was derived from Reactome, NCI/Nature Pathway Interaction Database, HPRD, and the MSKCC Cancer Cell Map. Submitted by Ethan Cerami, MSKCC. |
1.000 |
-- |
101 |
| PATHWAYS: GBM pathways |
Genes in the supplemental pathway figure of the TCGA GBM manuscript. Manually curated, based on a review paper by Furnari et al. [Pubmed] and additional literature and database searches. |
1.000 |
-- |
103 |
| PATHWAYS: Hippo pathway |
Key genes from the Hippo pathway. [Abstract]. Submitted by Li Ding. |
1.000 |
-- |
12 |
| PATHWAYS: KEGG COSMIC intersection |
List of all genes which exist in KEGG metabolic pathways AND in COSMIC. |
1.000 |
-- |
115 |
| PATHWAYS: KEGG metabolic pathways |
List of genes contained in metabolic pathways obtained from the KEGG database. Sent by Ethan Cerami and Nikolaus Schultz (MSKCC). |
1.000 |
-- |
1437 |
| PATHWAYS: Network Analysis: 2,3 altered neighbors |
Network analysis was used to score the neighborhood of each gene. Only those genes with 2 or 3 altered neighbors are included in this list. Alteration is determined by sequence mutation, high-level amplification or homozygous deletion in >5% of all cases. Network data was derived from Reactome, NCI/Nature Pathway Interaction Database, HPRD, and the MSKCC Cancer Cell Map. Submitted by Ethan Cerami, MSKCC. |
.500 |
-- |
444 |
| PATHWAYS: Network Analysis: >= 4 altered neighbors |
Network analysis was used to score the neighborhood of each gene. Only those genes with >=4 altered neighbors are included in this list. Alteration is determined by sequence mutation, high-level amplification or homozygous deletion in >5% of all cases. Network data was derived from Reactome, NCI/Nature Pathway Interaction Database, HPRD, and the MSKCC Cancer Cell Map. Submitted by Ethan Cerami, MSKCC. |
1.000 |
-- |
93 |
| PATHWAYS: Network Analysis: Sven Nelander |
Computational network analysis based on gene expression and copy number. From Sven Nelander at MSKCC (cBio) and the University of Gothenburg |
1.000 |
-- |
122 |
| PATHWAYS: P53 Network |
Contains a list of 71 p53 pathway genes, gathered from multiple p53 database and literature searches. Generally, they are p53 interacting proteins, direct p53 regulators, or key p53 target genes. They are ranked by the number of times they appear as mutated in the Discovery lists of three Vogelstein cancer genomics papers for GBM, pancreatic cancer, breast, and colorectal cancer. Many of the p53 pathway genes with 0 mutations were apparently not sequenced by the Vogelstein group. Submitted by Lawrence A. Donehower and David Wheeler, Baylor College of Medicine. |
1.000 |
-- |
70 |
| PATHWAYS: Wnt and NOTCH |
Wnt and NOTCH pathway associated genes. Submitted by Ruprecht Wiedemeyer from the DFCI. |
1.000 |
-- |
153 |
| RECENT STUDY: Hopkins Breast/colorectal cancer |
Parsons DW. et al, The genomic landscapes of human breast and colorectal cancers. Science. 2007 Nov 16;318(5853):1108-13. [PubMed]. |
1.000 |
-- |
272 |
| RECENT STUDY: Hopkins GBM |
Parsons DW et al., An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26;321(5897):1807-12 [PubMed]. |
1.000 |
-- |
42 |
| RECENT STUDY: Hopkins Pancreatic cancer |
Parsons DW et al., Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26;321(5897):1801-6. [PubMed]. |
1.000 |
-- |
23 |
| RECENT STUDY: TSP Lung adenocarcinoma |
Ding L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 Oct 23;455(7216):1069-75. [Pubmed]. |
1.000 |
-- |
26 |
| TCGA COPY NUMBER: RAE Regions of Interest |
MSKCC/UNC: Copy Number Genes. Includes genes resident in ROIs (regions of interest) of amplification and deletion identified by RAE with an FDR (q-value) < 10% (each ROI exceeded a random aberration rate that RAE constructs from the GBM data itself). Of the original 1,419 genes in ROIs, 945 were correlated in expression (66.6%). This list icludes only the 945 that correlated with expression. RAE analysis perform by Barry Taylor, MSKCC. Gene expression correlation performed by Katie Hoadley, UNC. |
1.000 |
-- |
943 |
| TCGA GENE EXPRESSION: Alternatively spliced genes (tumor vs normal) |
Alternatively spliced genes between tumors and normals. Sent by Paul Spellman from LBNL, Life Sciences division. |
1.000 |
-- |
48 |
| TCGA GENE EXPRESSION: Alternatively spliced genes associated to tumor subtype |
Alternatively spliced genes associated to tumor subtypes. Sent by Paul Spellman from LBNL, Life Sciences division. |
1.000 |
-- |
38 |
| TCGA GENE EXPRESSION: Differentially expressed between tumor and normal |
Top genes distinguishing Tumors (n=167) from Normal (n=14) samples. Sent by Katherine Hoadley and Neil Hayes from the Lineberger Comprehensive Cancer Center, UNC, Chapel Hill. Genes identified by ClaNC |
.500 |
-- |
488 |
| TCGA GENE EXPRESSION: Invasion-associated |
Genes differentially expressed from matched GBM core v invasive rim, or associated with GBM migration. Sent by Michael Berens of the Translational Genomics Research Institute. |
.500 |
-- |
863 |
| TCGA GENE EXPRESSION: Subtype analysis |
Genes identified by ClaNC (classification to nearest centroids) to predict the four gene expression subtypes. Sent by Katherine Hoadley and Neil Hayes from the Lineberger Comprehensive Cancer Center, UNC, Chapel Hill. |
.500 |
-- |
840 |
| TCGA GENE EXPRESSION: Variably expressed |
Top 500 variably expressed genes from the unified gene expression data set identified by genes with the highest MAD scores. Sent by Katherine Hoadley and Neil Hayes from the Lineberger Comprehensive Cancer Center, UNC, Chapel Hill. |
.500 |
-- |
500 |
| TCGA METHYLATION: Hypermethylated in GBM tumors |
Aberrantly hypermethylated genes from GBM tumors. Sent by Dan Weisenberger on behalf of Johns Hopkins University and the University of Southern California. |
1.000 |
-- |
207 |
| TCGA RESEQUENCE: 1 mutation |
Genes with a single somatic mutation in Phases I or II of TCGA GBM Sequencing |
.250 |
-- |
268 |
| TCGA RESEQUENCE: 2 or more mutations |
Genes with 2 or more somatic mutations in Phases I or II of TCGA GBM sequencing |
.750 |
-- |
160 |
| TCGA SEQUENCED: GBM phase 1 |
Target list for phase 1 of the TCGA GBM sequencing project |
.250 |
-- |
601 |
| TCGA SEQUENCED: GBM phase 2 |
Target list for phase 2 of the TCGA GBM sequencing project |
.250 |
-- |
649 |
| TCGA SEQUENCING: Exclude |
Genes to exclude from sequencing for various reasons (hard to map, pseudogenes, etc.). |
-1.000 |
-- |
24 |
