Dataset Information
PathBIX-a web server for network-based pathway annotation with adaptive null models.
Ontology highlight
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.Supplementary information
Supplementary data are available at Bioinformatics Advances online.
SUBMITTER: Castresana-Aguirre M
PROVIDER: S-EPMC9710673 | biostudies-literature | 2021
REPOSITORIES: biostudies-literature
Publications
PathBIX-a web server for network-based pathway annotation with adaptive null models.
Bioinformatics advances 20210701 1
<h4>Motivation</h4>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 compa ...[more]