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pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks

View ORCID ProfileEge Ulgen, Ozan Ozisik, View ORCID ProfileOsman Ugur Sezerman
doi: https://doi.org/10.1101/272450
Ege Ulgen
1Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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  • For correspondence: egeulgen@gmail.com
Ozan Ozisik
2Department of Computer Engineering, Electrical & Electronics Faculty, Yildiz Technical University, Istanbul, Turkey
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Osman Ugur Sezerman
1Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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  • ORCID record for Osman Ugur Sezerman
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Abstract

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

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 07, 2018.
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pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Ege Ulgen, Ozan Ozisik, Osman Ugur Sezerman
bioRxiv 272450; doi: https://doi.org/10.1101/272450
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pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Ege Ulgen, Ozan Ozisik, Osman Ugur Sezerman
bioRxiv 272450; doi: https://doi.org/10.1101/272450

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