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Updated: Aug 12, 2025
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
PathBIX-a web server for network-based pathway annotation with adaptive null models
Miguel Castresana-Aguirre1, Emma Persson1, Erik L L Sonnhammer1
1Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 17121, Sweden.
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.
Supplementary Information:
Supplementary data are available at Bioinformatics Advances online.
