Cancer Genome Anatomy Project

Abstract

The Cancer Genome Anatomy Project CGAP generates gene expression, polymorphism and chromosomal aberration datasets to support the elucidation of the molecular signatures of cancer. To facilitate use of CGAP data by the biomedical research community, the project has developed a suite of analytical tools designed to facilitate in silico analysis.

Keywords: genomics; gene expression; SAGE; SNPs; cytogenetics

Figure 1.

The Cancer Genome Anatomy Project Home Page.

Figure 2.

Example of the results obtained when using the Gene Expression Displayer (DGED) tool to query the SAGE gene expression data set. Under the Gene column are listed various SAGE tags that were present in the libraries selected in the search query, and that are about 10 nt in length. If a specific gene is associated with a SAGE tag, it is listed in the Gene column; however, not all tags correlate with a specific gene. The Library column displays the number of libraries in which the SAGE tag was represented at least one time, while the Tag column shows the total number of times that a tag appeared in all the libraries listed. The sequence odds ratio is the fraction of tag counts in pool A divided by the fraction of tags in pool B for an individual tag. In the examples shown, this is not calculated because the denominator is zero. Probability values are based on the Fisher exact test.

Figure 3.

Example of a display from the Virtual Northern tool, which includes data obtained from the DGED tool. This tool provides a visual display, as well as a numerical representation of the relative level of gene expression in various tissues. The numerator represents the number of times a SAGE tag was observed in that tissue, while the denominator shows the total number of tags represented in the samples analyzed. The Virtual Northern tool displays gene expression profiles from both the EST and SAGE data sets in the CGAP collection.

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References

Adams MD, Dubnick M, Kerlavage AR, et al. (1992) Sequence identification of 2375 human brain genes. Nature 355: 632–634.

Alizadeh AA, Eisen MB, Davis RE, et al. (2000) Distinct types of diffuse large B‐cell lymphoma identified by gene expression profiling. Nature 403: 503–511.

Brinkmann U, Vasmatzis G, Lee B and Pastan I (1999) Novel genes in the PAGE and GAGE family of tumor antigens found by homology walking in the dbEST database. Cancer Research 59: 1445–1448.

Clifford R, Edmonson M, Hu Y, et al. (2000) Expression‐based genetic/physical maps of single‐nucleotide polymorphisms identified by the cancer genome anatomy project. Genome Research 10: 1259–1265.

Druker BJ and Lydon NB (2000) Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia. Journal of Clinical Investigation 105: 3–7.

Kirsch IR, Green ED, Yonescu R, et al. (2000) A systematic, high‐resolution linkage of the cytogenetic and physical maps of the human genome. Nature Genetics 24: 339–340.

Lash AE, Tolstoshev CM, Wagner L, et al. (2000) SAGEmap: a public gene expression resource. Genome Research 10: 1051–1060.

Riggins GJ and Strausberg RL (2001) Genome and genetic resources from the Cancer Genome Anatomy Project. Human Molecular Genetics 10: 663–667.

Slamon DJ, Leyland‐Jones B, Shak S, et al. (2001) Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. New England Journal of Medicine 344: 783–792.

Strausberg RL (2001) The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer. Journal of Pathology 195 (1): 31–40.

Strausberg RL, Buetow KH, Emmert‐Buck MR and Klausner RD (2000) The Cancer Genome Anatomy Project: building an annotated gene index. Trends in Genetics 16: 103–106.

Velculescu VE, Zhang L, Vogelstein B and Kinzler KW (1995) Serial analysis of gene expression. Science 270: 484–487.

Further Reading

Cheung VG, Nowak N, Jang W, et al. (2001) Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409: 953–958.

Emmert‐Buck MR, Strausberg RL, Krizman DB, et al. (2000) Molecular profiling of clinical tissue specimens: feasibility and applications. American Journal of Pathology 156: 1109–1115.

Klausner RD (2002) The fabric of cancer biology: weaving together the strands. Cancer Cell 1: 3–10.

Perou CM, Sorlie T, Eisen MB, et al. (2000) Molecular portraits of human breast tumours. Nature 406: 747–752.

Weber BL (2002) Cancer genomics. Cancer Cell 1: 37–47.

Web Links

BioCarta www.Biocarta.com

CGAP (cancer genome anatomy project) http://cgap.nci.nih.gov

KEGG http://www.kegg.org/pathwaymaps

Mitelman Database of Chromosome Aberrations in Cancer http://cgap.nci.nih.gov/chromosomes/Mitelman

NCI Center for Bioinformatics http://ncicb.nci.nih.gov

OMIM (online Mendelian inheritance in man) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

UniGene http://www.ncbi.nlm.nih.gov/UniGene/

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How to Cite close
Strausberg, Robert L(Jan 2006) Cancer Genome Anatomy Project. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0006070]