This proposal addresses the continued support for maintenance and further development of the UCSD- Nature Signaling Gateway. The Signaling Gateway (www.signaling-gateway.org)is a collaboration between the University of California, San Diego and Nature Publishing Group (NPG) and is designed to facilitate navigation of the complex world of cell signaling research. The Signaling Gateway comprises three components: the Molecule Pages (MP), the Signaling Update and the Data Center. The Data Center is a legacy of the Alliance for Cellular Signaling and will merely be maintained at status quo. The Signaling Update, which provides short editorial highlights of recent signaling papers, a library of relevant publications, a conference calendar, and pertinent news stories, will continue to be updated on a weekly basis with fresh editorial content. The MPs provide regularly updated, essential information derived from public databases and sequence analysis on approximately 4000 mammalian proteins involved in signal transduction. In addition, 500 of these MPs contain published, expert-authored information about the protein. Published MPs contain both a full-text review article about the molecule and highly structured data for bioinformatics interrogation, including information on protein-protein and protein-ligand interactions, subcellular localization, post-translational modifications and biological or enzymatic activity. Importantly, NPG administers rigorous peer and editorial review of each published MP. The MP data are stored in an object-relational database format and are freely accessible to the authors, the reviewers and the public via a web interface that serves as a presentation layer. The MPs, Signaling Update and Data Center are routinely accessed by tens of thousands of members of the signal transduction community, both abroad and in the US, and remain a highly trusted and valuable resource for cell signaling researchers. In addition to providing continued maintenance for the Signaling Gateway, this proposal aims to expand the MPs to other species, publish updated versions of existing MPs, develop novel microRNA MPs, create complex query interfaces, introduce a new and interactive MP Wiki, and provide the ability to export an MP and its contents to other public repositories and to the larger user community.
Normal and pathophysiological function is controlled by biochemical processes in cells and tissues. Cellular responses to stimuli, including growth, differentiation, arrest and apoptosis are a consequence of cellular signaling and regulatory events. The Signaling Gateway is a project that captures our state-of- the-art knowledge of the signaling machinery;namely, the proteome that composes the molecular pathways that mediate defined physiological phenotypes. This project represents collaboration between an academic institution and a reputable publishing group and aims to create an expert-curated, peer- reviewed catalog of all mammalian signaling molecules and the myriad biological and biochemical pathways in which they participate. The Signaling Gateway, which is already widely used by the biomedical research community, will be expanded in scope to include the latest material on signaling proteins, an annotated database and expert-authored reviews of micro RNA molecules, an efficient query system and an ability to export the information in biologist-friendly as well as machine-readable formats. Most importantly, we propose to engage the larger biomedical research community in the rapid dissemination of new signaling-related techniques, reagents and data via a Wiki mechanism.
|Bhargava, Vipul; Head, Steven R; Ordoukhanian, Phillip et al. (2014) Technical variations in low-input RNA-seq methodologies. Sci Rep 4:3678|
|Gersten, Merril; Zhou, Dan; Azad, Priti et al. (2014) Wnt pathway activation increases hypoxia tolerance during development. PLoS One 9:e103292|
|Bhargava, Vipul; Ko, Pang; Willems, Erik et al. (2013) Quantitative transcriptomics using designed primer-based amplification. Sci Rep 3:1740|
|Yang, Kun; Dinasarapu, Ashok R; Reis, Edimara S et al. (2013) CMAP: Complement Map Database. Bioinformatics 29:1832-3|
|Subramaniam, Shankar; Fahy, Eoin; Gupta, Shakti et al. (2011) Bioinformatics and systems biology of the lipidome. Chem Rev 111:6452-90|
|Dinasarapu, Ashok Reddy; Saunders, Brian; Ozerlat, Iley et al. (2011) Signaling gateway molecule pages--a data model perspective. Bioinformatics 27:1736-8|
|Gupta, Shakti; Maurya, Mano Ram; Subramaniam, Shankar (2010) Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells. PLoS Comput Biol 6:e1000654|
|Green, Chad E; Liu, Tiffany; Montel, Valerie et al. (2009) Chemoattractant signaling between tumor cells and macrophages regulates cancer cell migration, metastasis and neovascularization. PLoS One 4:e6713|
|Saunders, Brian; Lyon, Stephen; Day, Matthew et al. (2008) The Molecule Pages database. Nucleic Acids Res 36:D700-6|