The cancer genome anatomy project: Web-based analysis tools for deciphering the molecular expression profiles of cancer

4803 The National Cancer Institute initiated the Cancer Genome Anatomy Project (CGAP), a multi-disciplinary program founded on the concept that each type of cancer has a unique gene expression profile. CGAP applies advanced technologies to enrich gene expression databases with expressed sequence tag (EST) and serial analysis of gene expression (SAGE) data from a variety of normal and cancerous tissues for both human and mouse. CGAP also develops web-based tools that enable the analysis of data from these vast molecular databases. Availability of robust molecular datasets and web-based analysis tools has provided the foundation necessary to support the delineation of the molecular profiles of normal and cancerous tissues. The CGAP web site (http://cgap.nci.nih.gov/) is designed to serve as an interface between genomics and cancer research. The home page provides access to gene expression data from various biological aspects. The “Genes” section provides on-line tools that can be used to analyze the expression profile of a single gene within tissues. This section includes access to databases listing single nucleotide polymorphisms identified in genes related to cancer. Tools in the “Tissues” section aid analysis of the gene expression profiles of various human and mouse tissues. For example, the “Digital Gene Expression Displayer” compares genes that are differentially expressed between various tissues. The “SAGE Genie” section examines gene expression profiles based on SAGE data and contains the “Anatomic SAGE Viewer”. This viewer displays the number of SAGE tags expressed for a selected gene in tissues by varying intensities of color. In addition to the collection of tools to study gene expression, the “Pathways” portal provides information for genes that play a role in various biological pathways. CGAP is currently supporting an RNAi (RNA interference) project that will generate RNAi clones for human and mouse genes. This project promises to generate valuable reagents for the experimental study of gene function in mammalian cells. CGAP has endeavored to provide a comprehensive database, informatic tools, and clone resources that assist both basic and clinical investigators in defining and characterizing the molecular profiles of cancer cells, with anticipated applications in all areas of cancer research.