title: iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data.
abstract: Pathway analyses help reveal underlying molecular mechanisms of complex biological phenotypes. Biologists tend to perform multiple pathway analyses on the same dataset, as there is no single answer. It is often inefficient for them to implement and/or install all the algorithms by themselves. Online tools can help the community in this regard. Here we present an online gene expression analytical tool called iCOSSY which implements a novel pathway-based COntext-specific Subnetwork discoverY (COSSY) algorithm. iCOSSY also includes a few modifications of COSSY to increase its reliability and interpretability. Users can upload their gene expression datasets, and discover important subnetworks of closely interacting molecules to differentiate between two phenotypes (context). They can also interactively visualize the resulting subnetworks. iCOSSY is a web server that finds subnetworks that are differentially expressed in two phenotypes. Users can visualize the subnetworks to understand the biology of the difference.
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.
authors.forename: Ashis
authors.initials: A
authors.lastname: Saha
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea.
authors.forename: Minji
authors.initials: M
authors.lastname: Jeon
authors.affiliation: Department of Medicine/Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America.
authors.forename: Aik Choon
authors.initials: AC
authors.lastname: Tan
authors.affiliation: Department of Computer Science and Engineering, Korea University, Seoul, Korea; Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, Korea.
authors.forename: Jaewoo
authors.initials: J
authors.lastname: Kang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D015870:Gene Expression; D053263:Gene Regulatory Networks; D020407:Internet; D010641:Phenotype; D025941:Protein Interaction Mapping / Q000379:methods*