Reconstructing signaling pathways using regular language constrained paths.

ABSTRACT:

Motivation

High-quality curation of the proteins and interactions in signaling pathways is slow and painstaking. As a result, many experimentally detected interactions are not annotated to any pathways. A natural question that arises is whether or not it is possible to automatically leverage existing pathway annotations to identify new interactions for inclusion in a given pathway.

Results

We present RegLinker, an algorithm that achieves this purpose by computing multiple short paths from pathway receptors to transcription factors within a background interaction network. The key idea underlying RegLinker is the use of regular language constraints to control the number of non-pathway interactions that are present in the computed paths. We systematically evaluate RegLinker and

SUBMITTER: Wagner MJ 

PROVIDER: S-EPMC6612893 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature