PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping

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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 knowledgebases. However, the isoform and post-translational modification states of proteins are lost when converting input and pathways into gene-centric lists.

Findings

Based on the Reactome knowledgebase, 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, and pathways.

Conclusions

PathwayMatcher enables refining the network-representation of pathways by including isoform and post-translational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity and it becomes possible to distinguish interactions between different forms of the same protein.

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  1. A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz088), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102978

    Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102979

    Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102980

    Reviewer 4: http://dx.doi.org/10.5524/REVIEW.102981