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PAFway: pairwise associations between functional annotations in biological networks and pathways.

ABSTRACT:

Motivation

Large gene networks can be dense and difficult to interpret in a biologically meaningful way.

Results

Here, we introduce PAFway, which estimates pairwise associations between functional annotations in biological networks and pathways. It answers the biological question: do genes that have a specific function tend to regulate genes that have a different specific function? The results can be visualized as a heatmap or a network of biological functions. We apply this package to reveal associations between functional annotations in an Arabidopsis thaliana gene network.

Availability and implementation

PAFway is submitted to CRAN. Currently available here: https://github.com/ezer/PAFway.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Mahjoub M

PROVIDER: S-EPMC7750965 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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PAFway: pairwise associations between functional annotations in biological networks and pathways.

Mahjoub Mahiar M Ezer Daphne D

Bioinformatics (Oxford, England) 20201201 19

<h4>Motivation</h4>Large gene networks can be dense and difficult to interpret in a biologically meaningful way.<h4>Results</h4>Here, we introduce PAFway, which estimates pairwise associations between functional annotations in biological networks and pathways. It answers the biological question: do genes that have a specific function tend to regulate genes that have a different specific function? The results can be visualized as a heatmap or a network of biological functions. We apply this packa ...[more]

PMID: 32678900

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