Achievement

IGERT trainee Jignesh Parikh in (Discovering causal signaling pathways through gene expression patterns using SPEED: Parikh JR, Klinger B, Xia Y, Marto JA, Blüthgen N, Nucleic Acids Research, 2010, 38 Web Server issue: W109-17) presents an intuitive approach for discovering upstream signaling pathways responsible for regulating differentially expressed genes as opposed to the more common approach of searching for significant membership of translated proteins in various signaling pathways. We identify consistently regulated signature genes specific for signaling pathways from a panel of single-pathway perturbation experiments. An algorithm that detects overrepresentation of these signature genes is used to infer the signaling pathway responsible for regulation. We expose our novel resource and algorithm through a web server called SPEED: Signaling Pathway Enrichment using Experimental Datasets. SPEED can be freely accessed at: http://speed.sys-bio.net/