||September 25, 2007
||Dr. John N. Weinstein, Genomics & Bioinformatics Group, National Cancer Institute
||The Miner Suite and its Application to Cancer: Bioinformatic Resources that Complement KEGG
The underlying hypothesis of what we have termed “integromics” is that different types of molecular information can combine “synergistically.” One example is our research  using the panel of 60 human cancer cell lines (NCI-60) used by the U.S. NCI to screen >100,000 compounds for anticancer activity. We and our collaborators have profiled those cells extensively at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels using >15 microarray platforms overall. To aid in integrating the different types of molecular information, we have been developing the Miner Suite of publicly available web-based bioinformatic tools and molecular profile databases. Included to date are MedMiner, CIMminer, GoMiner, High-throughput GoMiner, CellMiner, MIMminer, SmudgeMiner, MatchMiner, and AbMiner. The most recent tool, SpliceMiner, is an engine for dealing with splice variation . The Miner Suite complements the very impressive KEGG pathway databases and bioinformatic tools. In 2006, we and our collaborators launched the “Spotlight on Molecular Profiling” series [2-4] in Molecular Cancer Therapeutics to make the tools and profile data widely available for an integrative, systems-oriented approach to drug and biomarker discovery as part of the drive toward “personalized medicine” [6,7].
1. Weinstein, et al. An information-intensive approach... Science 1997; 275:343.
2. Weinstein, Spotlight on molecular profiling: ‘integromic’... Mol. Ca. Ther. 2006;5:2601.
3. Lorenzi, et al., Asparagine synthetase as a biomarker… ibid 2006;5:2613.
4. Ikediobi, et al., Mutation analysis… ibid 2006;5:2606.
5. Kahn, SpliceMiner... BMC Bioinformatics 2007;8:75.
6. Ludwig and Weinstein, Biomarkers… Nature Reviews Cancer 2005;5:845.
7. Lee, et al. A new strategy for predicting chemosensitivity... PNAS 2007;104;13086.