NAR Molecular Biology Database Collection entry number 951
Higgins ME, Claremont M, Major JE, Sander C, Lash AE
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

Database Description

The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order to study their association with disease and their direct effects on gene function. Since the description of tumor suppressor genes and oncogenes several decades ago, both germ-line variations and somatic mutations have been established to be important in cancer in terms of risk, oncogenesis, prognosis, and response to therapy. The Cancer Genome Atlas (TCGA) initiative proposed by the NIH is poised to elucidate the contribution of somatic mutations to cancer development and progression through the re-sequencing of a substantial fraction of the total collection of human genes—in hundreds of individual tumors and spanning several tumor types. We have developed the CancerGenes resource to simplify the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases. Each gene is annotated with gene name(s), functional description, organism, chromosome number, location, Entrez Gene ID, GO terms, InterPro descriptions, gene structure, protein length, transcript count, and experimentally determined transcript control regions, as well as links to Entrez Gene, COSMIC, and iHOP gene pages and the UCSC and Ensembl genome browsers. The user-friendly interface provides for searching, sorting and intersection of gene lists. Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table.


We gratefully acknowledge the efforts of Marc Ladanyi and Doron Betel in the critical review of a preliminary implementation of CancerGenes and their helpful suggestions. In addition, we thank Marc Ladanyi for contributing his domain knowledge.


1. International HapMap Consortium. (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
2. Bignell, G., Smith, R., Hunter, C., Stephens, P., Davies, H., Greenman, C., Teague, J., Butler, A., Edkins, S., Stevens, C., et al. (2006) Sequence analysis of the protein kinase gene family in human testicular germ-cell tumors of adolescents and adults. Genes Chromosomes Cancer, 45, 42-46.
3. Davies, H., Hunter, C., Smith, R., Stephens, P., Greenman, C., Bignell, G., Teague, J., Butler, A., Edkins, S., Stevens, C., et al. (2005) Somatic mutations of the protein kinase gene family in human lung cancer. Cancer Research, 65, 7591-7595.
4. Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., Stratton, M.R. (2004) A census of human cancer genes. Nature Reviews Cancer, 4,177-183.
5. Stephens, P., Edkins, S., Davies, H., Greenman, C., Cox, C., Hunter, C., Bignell, G., Teague, J., Smith, R., Stevens, C., et al. (2005) A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nature Genetics, 37, 590-592.
6. Forbes, S., Clements, J., Dawson, E., Bamford, S., Webb, T., Dogan, A., Flanagan, A., Teague, J., Wooster, R., Futreal, P.A., Stratton, M.R. (2006) COSMIC 2005. British Journal of Cancer, 94, 318-322.
7. Hahn, W.C., Weinberg, R.A.. (2002) Modeling the molecular circuitry of cancer. Nature Reviews Cancer, 2, 331-341.
8. Vogelstein, B., Kinzler, K.W. (2004) Cancer genes and the pathways they control. Nature Medicine, 10, 789-799.
9. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 34, D173-D180.
10. Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., Birney, E. (2004) EnsMart: a generic system for fast and flexible access to biological data. Genome Research, 14, 160-169.
11. Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., Ren, B. (2005) A high-resolution map of active promoters in the human genome. Nature, 436, 876-880.
12. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res., 33, D201-D205.
13. Mitelman, F. Recurrent chromosome aberrations in cancer. (2000) Mutation Research, 462, 247-253.

Subcategory: Cancer gene databases

Go to the article in the NAR Database issue.
Oxford University Press is not responsible for the content of external internet sites