PathBIX - a web server for network-based pathway annotation with adaptive null models

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Abstract

Motivation: Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, utilize biological networks to gain a richer source of information as a basis of the analysis than merely the gene content. Network-based methods use the network crosstalk between the query gene set and the genes in known pathways, and compare this to a null model of random expectation. Results: We developed PathBIX, a novel web application for network-based pathway analysis, based on the recently published ANUBIX algorithm which has been shown to be more accurate than previous network-based methods. The PathBIX website performs pathway annotation for 21 species, and utilizes prefetched and preprocessed network data from FunCoup 5.0 networks and pathway data from three databases: KEGG, Reactome, and WikiPathways. Availability: https://pathbix.sbc.su.se/ Contact: erik.sonnhammer@scilifelab.se

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Castresana-Aguirre, M., Persson, E., & Sonnhammer, E. L. L. (2021). PathBIX - a web server for network-based pathway annotation with adaptive null models. Bioinformatics Advances, 1(1). https://doi.org/10.1093/bioadv/vbab010

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