This proposal addresses the continued maintenance and enhancement of the Cellular Signaling-Nature Signaling Gateway (SG). SG was initiated under the Alliance for Cellular Signaling (AfCS) Project in 2000. It contains the Signaling Update - updates on articles and news concerning cellular signaling made freely available to the research community by the Nature Publishing Group (NPG), the Molecule Pages Database (MPDB) - a comprehensive expert-authored and peer-reviewed resource on signaling molecules, and the Data Center - a compendium of data on two mammalian cell types measured in the Alliance for Cellular Signaling experimental laboratories. SG has been a very successful research infrastructure project and is arguably one of the most used resources in the cell signaling research discipline. The proposal will address the continued maintenance and enhancement of the SG site. In addition to extending the capability and the accessibility of the Molecule Pages (including versioning and data tracking of MP), it is proposed to extend the MPDB to non-mouse species with expert author entered data on human, rat and other mammalian species proteins. Other major aspects of this proposal include opening of the Data Center to non-AfCS data through easy entry mechanisms, and creation of an interoperable query infrastructure that will enable a researcher query across the content of MP and the diverse and heterogeneous data presented in the Data Center. It is expected that this will be a valuable cellular systems biology resource where """"""""what if"""""""" queries across data can provide new insights and sometimes knowledge. It is also proposed to provide seamless dissemination and query tools for the community with a range of options from visualizing or downloading of specific data on the SG site to downloading large datasets or entire sections to creating total mirrors of the SG site. It is anticipated that the SG will become a very useful research resource in biomedicine. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM078005-02
Application #
7291631
Study Section
Special Emphasis Panel (ZRG1-BST-L (51))
Program Officer
Lyster, Peter
Project Start
2006-09-30
Project End
2009-08-31
Budget Start
2007-09-01
Budget End
2008-08-31
Support Year
2
Fiscal Year
2007
Total Cost
$472,294
Indirect Cost
Name
University of California San Diego
Department
Engineering (All Types)
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
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