The PathLinker app: Connect the dots in protein interaction networks [version 1; peer review: 1 approved, 2 approved with reservations]

PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. We originally developed PathL...

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Bibliographic Details
Published inF1000 research Vol. 6; p. 58
Main Authors Gil, Daniel P, Law, Jeffrey N, Murali, T. M
Format Journal Article
LanguageEnglish
Published England Faculty of 1000 Ltd 2017
F1000Research
F1000 Research Ltd
Subjects
Bioinformatics
Software Tool
PathLinker
Cytoscape
k-shortest paths
signaling pathways
protein interaction networks
pathway reconstruction
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Summary:PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. We originally developed PathLinker to complement manual curation of signaling pathways, which is slow and painstaking. The method can be used in general to connect any set of sources to any set of targets in an interaction network. The app presented here makes the PathLinker functionality available to Cytoscape users. We present an example where we used PathLinker to compute and analyze the network of interactions connecting proteins that are perturbed by the drug lovastatin.
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DPG implemented and tested the Cytoscape app. JNL performed the lovastatin analysis. TMM proposed the development of the P athL inker app and the lovastatin analysis, and supervised DPG and JNL. All three authors wrote the paper.
Competing interests: No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.9909.1