SteinerNet: a web server for integrating ‘omic’ data to discover hidden components of response pathways
Name
Tuncbag-2012-SteinerNet_ a web se.pdf
Size
2.61 MB
Format
Adobe PDF
Checksum (MD5)
39220b3617c5d5a37179f2abdbd63668
Author(s)
Tuncbag, Nurcan
McCallum, Scott
Huang, Shao-shan Carol
Fraenkel, Ernest
Date Issued
May 2012
Journal
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
Abstract
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.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/nar/gks445
