Abstract
The applications of functional genomics, proteomics and informatics to cancer research have yielded a tremendous amount of information, which is growing all the time. Much of this information is available publicly on the Internet and ranges from general information about different cancers from a patient or clinical viewpoint, through to databases suitable for cancer researchers of all backgrounds, to very specific sites dedicated to individual genes or molecules. A simple search for ‘cancer’ from a typical Web browser search engine yields more than half a million hits; an even more specific search for ‘leukaemia’ (>40 000 hits) or ‘p53’ (>5700 hits) yields far too many hits to allow one to identify particular sites of interest. This review aims to provide a brief guide to some of the resources and databases that can be used as springboards to home in rapidly on information relevant to many fields of cancer research. As such, this article will not focus on a single website but hopes to illustrate some of the ways that postgenomic biology is revolutionizing cancer research. It will cover genomics and proteomics approaches that have been applied to studying global expression patterns in cancers, in addition to providing links ranging from general information about cancer to specific cancer gene mutation databases.
Highlights
The applications of functional genomics, proteomics and informatics to cancer research have yielded a tremendous amount of information, which is growing all the time
There are many ways to focus in rapidly on general and cancer-related information about an individual gene using the resources at the National Centre for Biotechnology Information (NCBI)—an impressively curated, comprehensively integrated set of resources that allow a rapid and thorough trawl of gene-related data
The stated aim of Cancer Genome Anatomy Project (CGAP) at the National Cancer Institute is to define the molecular anatomy of a cancer cell, in particular to define which genes are expressed in cancers
Summary
There are many ways to focus in rapidly on general and cancer-related information about an individual gene using the resources at the NCBI—an impressively curated, comprehensively integrated set of resources that allow a rapid and thorough trawl of gene-related data. The UniGene entry links to gene and complete mRNA sequences and includes a selected list of homologues, ranked by identity at the protein level (with links to database entries) It supplies cytogenetic information (with a link to a close-up of the chromosomal region via OMIM) and expression information, defined by the cDNA library source of each of the clustered ESTs, in addition to links to SAGE data (see below). One drawback of this automated system that should be noted is that it http://www.ncbi.nlm.nih.gov/LocusLink/ LocusLink provides a curated information resource centred around the queried genetic locus (e.g. b-catenin entry, 1499). Facts are returned grouped under a variety of headings, e.g. cell cycle, clinical, function, phenotype, reviews, tumour incidence, and are linked to the PubMed entry of the reference paper
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