SteinerNet: a web server for integrating ‘omic’ data to discover hidden components of response pathways
Author(s)
Tuncbag, Nurcan; McCallum, Scott; Huang, Shao-shan Carol; Fraenkel, Ernest
DownloadTuncbag-2012-SteinerNet_ a web se.pdf (2.614Mb)
PUBLISHER_CC
Publisher with Creative Commons License
Creative Commons Attribution
Terms of use
Metadata
Show full item recordAbstract
High-throughput technologies including transcriptional profiling, proteomics and reverse genetics screens provide detailed molecular descriptions of cellular responses to perturbations. However, it is difficult to integrate these diverse data to reconstruct biologically meaningful signaling networks. Previously, we have established a framework for integrating transcriptional, proteomic and interactome data by searching for the solution to the prize-collecting Steiner tree problem. Here, we present a web server, SteinerNet, to make this method available in a user-friendly format for a broad range of users with data from any species. At a minimum, a user only needs to provide a set of experimentally detected proteins and/or genes and the server will search for connections among these data from the provided interactomes for yeast, human, mouse, Drosophila melanogaster and Caenorhabditis elegans. More advanced users can upload their own interactome data as well. The server provides interactive visualization of the resulting optimal network and downloadable files detailing the analysis and results. We believe that SteinerNet will be useful for researchers who would like to integrate their high-throughput data for a specific condition or cellular response and to find biologically meaningful pathways. SteinerNet is accessible at http://fraenkel.mit.edu/steinernet.
Date issued
2012-05Department
Massachusetts Institute of Technology. Department of Biological EngineeringJournal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Citation
Tuncbag, N. et al. “SteinerNet: a Web Server for Integrating ‘Omic’ Data to Discover Hidden Components of Response Pathways.” Nucleic Acids Research 40.W1 (2012): W505–W509.
Version: Final published version
ISSN
0305-1048
1362-4962