Table 1.
Resources and databases for oncogenomics
| Name | Description | Web address |
|---|---|---|
| Mutations in cancer | ||
| IARC TP53 mutation database | Compiles all TP53 gene variations identified in human populations and tumor samples. Data compiled from peer-reviewed literature and generalist databases. | http://www-p53.iarc.fr |
| EGFR mutations database | Comprehensive compendium of all somatic mutations in EGFR that have been identified in human cancers and reported in peer-reviewed literature. | http://www.somaticmutations-egfr.org/ |
| Breast cancer mutations database | Central repository for information regarding mutations and polymorphisms in breast cancer susceptibility genes. | http://research.nhgri.nih.gov/bic/ |
| COSMIC | Catalogue of Somatic Mutations in Cancer. | http://www.sanger.ac.uk/genetics/CGP/cosmic |
| Structural alterations in cancer | ||
| Progenetix | Overview of copy-number abnormalities in human cancer from CGH experiments. A curated database, it collects genomic gain/loss information of individual cancer and leukemia cases published in peer-reviewed journals. | http://www.progenetix.net/progenetix |
| Mitelman database of chromosome aberrations in cancer | Relates chromosomal aberrations to tumor characteristics, based on either individual cases or associations. | http://cgap.nci.nih.gov/Chromosomes/Mitelman |
| NCBI/NCI's cancer chromosomes | Integrates NCI/NCBI SKY/M-FISH and CGH database, NCI Mitelman database of chromosome aberrations in cancer, and NCI recurrent aberrations in cancer database. | http://www.ncbi.nlm.nih.gov/sites/entrez?db=cancerchromosomes |
| DNA methylation alterations in cancer | ||
| MethyCancer | Database of human DNA methylation and cancer; it collects data from other public databases and resources and integrates this information with CpG island prediction and expression data. | http://methycancer.psych.ac.cn |
| Transcriptomic alterations in cancer | ||
| GEO | Gene-expression/molecular abundance repository supporting MIAME-compliant data submissions and a curated, online resource for gene-expression data browsing, query, and retrieval. Not specific for cancer, but contains many cancer data sets. | http://www.ncbi.nlm.nih.gov/geo/ |
| ArrayExpress | Public archive for transcriptomics data aimed at storing MIAME- and MINSEQE-compliant data in accordance with MGED recommendations. ArrayExpress Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the archive. Like GEO, not specific for cancer but contains many cancer data sets. | http://www.ebi.ac.uk/microarray-as/ae/ |
| Oncomine | Cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses. | http://www.oncomine.org/ |
| Integrative projects | ||
| The Cancer Genome Atlas | Comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through application of genome analysis technologies, including large-scale genome sequencing. | http://tcga.cancer.gov/ |
| Cancer Genome Project | Sanger Center Project aimed at identifying somatically acquired sequence variants/mutations and, hence, genes critical in the development of human cancers. | http://www.sanger.ac.uk/genetics/CGP/ |
| International Cancer Genome Consortium | International consortium with the goal of obtaining comprehensive description of genomic, transcriptomic, and epigenomic changes in 50 different tumor types and/or subtypes of clinical and societal importance across the globe. | http://www.icgc.org/ |
| NCI-CGAP | Interdisciplinary program established and administered by the NCI to generate information and technological tools needed to decipher molecular anatomy of the cancer cell. | http://www.ncbi.nlm.nih.gov/ncicgap/ |
| Integrative resources | ||
| IntOGen | Discovery tool for cancer researchers; integrates multidimensional OncoGenomics Data for the identification of genes and groups of genes (biological modules) involved in cancer development. | http://www.intogen.org |
| UCSC Cancer Genomics Browser | Suite of web-based tools to integrate, visualize, and analyze cancer genomics and clinical data. Displays a whole-genome and pathway-oriented view of genome-wide experimental measurements for individual and sets of samples alongside their associated clinical information. | http://genome-cancer.ucsc.edu |
| Other resources | ||
| Cancer Gene Census | Ongoing effort to catalog those genes for which mutations have been causally implicated in cancer. | http://www.sanger.ac.uk/genetics/CGP/Census/ |
| CancerGenes | Resource to simplify the process of gene selection and prioritization in large collaborative projects. Combines gene lists annotated by experts with information from key public databases. | http://cbio.mskcc.org/CancerGenes |
| CGPrio | Resource for the prioritization of candidate cancer genes after genomic experiments. Prioritization of oncogenes and tumor suppressor genes is based on computational classifiers that use different combinations of sequence and functional data, including sequence conservation, protein domains and interactions, and regulatory data. | http://bg.upf.edu/cgprio |
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Abbreviations: CGH: Comparative genomic hybridization; EGFR: Epidermal growth factor receptor; MGED: Microarray Gene Expression Database; MIAME: Minimum information about a microarray experiment; MINSEQE: Minimum information about a high-throughput sequencing experiment; NCBI: National Center for Biotechnology Information; NCI: National Cancer Institute
