Integrating protein localization with automated signaling pathway reconstruction.

ABSTRACT:

Background

Understanding cellular responses via signal transduction is a core focus in systems biology. Tools to automatically reconstruct signaling pathways from protein-protein interactions (PPIs) can help biologists generate testable hypotheses about signaling. However, automatic reconstruction of signaling pathways suffers from many interactions with the same confidence score leading to many equally good candidates. Further, some reconstructions are biologically misleading due to ignoring protein localization information.

Results

We propose LocPL, a method to improve the automatic reconstruction of signaling pathways from PPIs by incorporating information about protein localization in the reconstructions. The method relies on a dynamic program to ensure that the proteins

SUBMITTER: Youssef I 

PROVIDER: S-EPMC6886211 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature