The PathLinker app: Connect the dots in protein interaction networks

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Date
2017-01-20
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F1000Research
Abstract

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.

Description
Keywords
signaling pathways, pathway reconstruction, protein interaction networks, PathLinker, Cytoscape, k-shortest paths
Citation
Gil DP, Law JN and Murali TM. The PathLinker app: Connect the dots in protein interaction networks [version 1; peer review: 1 approved, 2 approved with reservations] F1000Research 2017, 6:58 https://doi.org/10.12688/f1000research.9909.1