Cancer Genome Anatomy Project


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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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


CGAP (cancer genome anatomy project)


Mitelman Database of Chromosome Aberrations in Cancer

NCI Center for Bioinformatics

OMIM (online Mendelian inheritance in man)



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