Pathway Pandemonium
By Kevin Davies
Bio-IT World
BOSTON (12/15/03)—This smorgasbord of signaling pathways and protein networks is one example of the remarkable work of researchers at the Institute of Bioinformatics in Bangalore, India, who together with Akhilesh Pandey, Aravinda Chakravarti, and colleagues at the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University, have created the new Human Protein Reference Database (HPRD).
Built using open-source technology, the freely available object database (www.hprd.org) aims to provide information not currently contained in Swiss-Prot, RefSeq, and other popular data repositories. HPRD contains information on thousands of protein-protein interactions, sites of expression, chemical modifications, and disease relevance — information that was manually collated and annotated by a team of some two dozen scientists in Bangalore sifting through more than 300,000 published articles!
The illustration below, taken from a paper in the October issue of Genome Research, depicts the pathways generated by activation of the EGF receptor (the target of drugs such as Herceptin and Iressa). Proteins in red boxes are major signaling molecules; small circles represent their interactors. Clicking any node links to the corresponding entry in HPRD.
The authors say that "before the power of systems biology can be fully harnessed, [the key issue] is to integrate genomic and proteomic data efficiently along with other sources of information such as the published literature. This integration will translate raw data into useful information, thereby expanding our knowledge about organisms." One immediate priority, for example, is to integrate publicly available microarray expression data.
PHOTO OF TREE/CHART BY S. PERI ET AL. GENOME RESEARCH 13, 2363-2371; 2003.
