PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping.

ABSTRACT:

Background

Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and posttranslational modification states of proteins are lost when converting input and pathways into gene-centric lists.

Findings

Based on the Reactome knowledge base, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input and outputs the possibly affected biochemical reactions, subnetworks, an

SUBMITTER: Sanchez LFH 

PROVIDER: S-EPMC6667378 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature