Journal Article

ProteinWeaver: A webtool to visualize ontology-annotated protein networks

Norman, Ainsley, Barelvi, Altaf, Anderson, Oliver, O’Brien, Aden, Jan, Iris, Ritz, Anna

2025

Overview

Molecular interaction networks are a vital tool for studying biological systems. While many tools exist that visualize a protein or a pathway within a network, no tool provides the ability for a researcher to consider a protein’s position in a network in the context of a specific biological process or pathway. We developed ProteinWeaver, a web-based tool designed to visualize and analyze non-human protein interaction networks by integrating known biological functions. ProteinWeaver provides users with an intuitive interface to situate a user-specified protein in a user-provided biological context (as a Gene Ontology term) in seven model organisms. ProteinWeaver also reports the presence of physical and regulatory network motifs within the queried subnetwork and statistics about the protein’s distance to the biological process or pathway within the network. These insights can help researchers generate testable hypotheses about the protein’s potential role in the process or pathway under study. Two cell biology case studies demonstrate ProteinWeaver’s potential to generate hypotheses from the queried subnetworks. ProteinWeaver is available at https://proteinweaver.reedcompbio.org/ .

• Publisher: Public Library of Science,PLOS,Public Library of Science (PLoS)
• Subject: Algorithms / Analysis / Animals / Annotations / Biological activity / Biology and Life Sciences / Computational Biology - methods / Computer and Information Sciences / Gene Ontology / Graph representations / Humans / Hypotheses / Insects / Internet / Molecular interactions / Networks / Ontology / Organisms / Protein Interaction Mapping - methods / Protein Interaction Maps / Protein-protein interactions / Proteins / Proteins - metabolism / Research and Analysis Methods / Software / Visualization / Web applications