RT Journal Article
SR Electronic
T1 pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 272450
DO 10.1101/272450
A1 Ege Ulgen
A1 Ozan Ozisik
A1 Osman Ugur Sezerman
YR 2018
UL http://biorxiv.org/content/early/2018/03/07/272450.abstract
AB Summary PathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies gene sets that form active subnetworks in a protein-protein interaction network using a list of genes provided by the user. It then performs pathway enrichment analyses on the identified gene sets. Further, using the R package pathview, it maps the user data on the enriched pathways and renders pathway diagrams with the mapped genes. Because many of the enriched pathways are usually biologically related, pathfindR also offers functionality to cluster these pathways and identify representative pathways in the clusters. PathfindR is built as a stand-alone package but it can easily be integrated with other tools, such as differential expression/methylation analysis tools, for building fully automated pipelines. In this article, an overview of pathfindR is provided and an example application on a rheumatoid arthritis dataset is presented and discussed.Availability The package is freely available under MIT license at: https://github.com/egeulgen/pathfindR