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DecoPath: A web application for decoding pathway enrichment analysis

: Mubeen, Sarah; Bharadhwaj, Vinay; Gadiya, Yojana; Hofmann-Apitius, Martin; Kodamullil, Alpha; Domingo-Fernández, Daniel

Fulltext urn:nbn:de:0011-n-6406332 (2.4 MByte PDF)
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Created on: 28.9.2021

NAR Genomics and bioinformatics 3 (2021), No.3, Art. lqab087, 9 pp.
ISSN: 2631-9268
Journal Article, Electronic Publication
Fraunhofer SCAI ()
pathway database; pathway enrichment; web application; bioinformatics software; Omics data

The past decades have brought a steady growth of pathway databases and enrichment methods. However, the advent of pathway data has not been accompanied by an improvement in interoperability across databases, hampering the use of pathway knowledge from multiple databases for enrichment analysis. While integrative databases have attempted to address this issue, they often do not account for redundant information across resources. Furthermore, the majority of studies that employ pathway enrichment analysis still rely upon a single database or enrichment method, though the use of another could yield differing results. These shortcomings call for approaches that investigate the differences and agreements across databases and methods as their selection in the design of a pathway analysis can be a crucial step in ensuring the results of such an analysis are meaningful. Here we present DecoPath, a web application to assist in the interpretation of the results of pathway enrichment analysis. DecoPath provides an ecosystem to run enrichment analysis or directly upload results and facilitate the interpretation of results with custom visualizations that highlight the consensus and/or discrepancies at the pathway- and gene-levels. DecoPath is available at, and its source code and documentation can be found on GitHub at