Creating efficient, uniform databasing and datasharing systems is critical for a vibrant computational biology network. For example, Ingenuity Systems (www.ingenuity.com) has developed a structured knowledge frameworka concept that won the 1998 Stanford University's BASES Entrepreneur's Challenge.
Core data are harvested from peer-reviewed journal articles, curated by Ph.D. scientists extracting findings based on an extensive ontology that spans molecules (genes, proteins, small molecules), biological processes at the cellular level (DNA damage, cell differentiation, adhesion, etc.) and at the organismal level (hepatotoxicity, knock-out phenotypes, disease, etc.).
Ingenuity Pathways Analysis (IPA) is a product that provides scientists with a set of tools that helps users better understand biological mechanisms based on genomic and proteomic experiments. IPA is for scientists working across the life sciences from early research to development and clinical applications.
Megan Laurance, Ph.D., Ingenuity product research scientist, explains that "one of our customers, Paul Mischel, M.D., at UCLA, is using genome-wide expression analysis on patient samples to identify genes and proteins that are perturbed in glioblastoma. "Dr. Mischel's goal is to identify new markers of glioblastoma, as well as novel therapeutic targets."
(For a recent review see "DNA-microarray analysis of brain cancer: molecular classification for therapy," Nat Rev Neurosci 10:782-92.)
According to Dr. Laurance, Dr. Mischel's use of IPA highlighted a pathway that contained known markers and targets of glioblastoma. What was unexpected was that in the middle of the pathway a gene was found that had never before been implicated as a key player in glioblastoma.
"So he went from a large set of data to confirming various aspects of the glioblastoma disease model to discovering a new potential target rather quickly," notes Dr. Laurance.
"Armed with practical mechanistic information about that pathway, he went back into the lab and used a variety of techniques (phosphotyrosine blots, RT-PCR, siRNA) to confirm the role of that gene in glioblastoma," says Dr. Laurance.