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A system for the integration and analysis of heterogeneous functional genomics data.

Web Application: https://www.geneweaver.org

API Documentation: https://geneweaver.jax.org/api/docs

What Is GeneWeaver?

GeneWeaver is a web application for the integrated cross-species analysis of functional genomics data from heterogeneous sources. The application consists of a large database of gene sets curated from multiple public data resources and curated submissions, along with a suite of analysis tools designed to allow flexible, customized workflows through web-based interactive analysis or scripted API driven analysis. Gene sets come from multiple widely studied species and include ontology annotations, brain gene expression atlases, systems genetic study results, gene regulatory information, pathway databases, drug interaction databases and many other sources. Users can retrieve, store, analyze and share gene sets through a graded access system. Gene sets and analysis results can be stored, shared and compared privately, among user defined groups of investigators, and across all users. Analysis tools are based on combinatorics and statistical methods for comparing, contrasting and classifying gene sets based on their members.

What Is a Gene Set?

Each "gene set" contains a list of genomic features, free text descriptive content, ontology annotations and gene association scores. Genomic features are mapped within and across multiple species. Currently, 10 species are supported, Mus musculus, Homo sapiens, Rattus norvegicus, Danio rerio, Drosophilia melanogaster, Macaca mulatta, Caenorhabditis elegans, Saccharomyces cervisiae, Gallus gallus, Canis familiaris. Additional species are added in response to community request.

What Can You Do With GeneWeaver?

GeneWeaver allows users to integrate these diverse functional genomics data across species, tissue and experimental platform to address questions about the relations among genes and biological functions. Applications include the prioritization of gene-disease associations from multiple evidence sources, the classification and comparison of biological functions based on biological substrates, and the identification of similar genes based on function. Cross species analysis enables the discovery of conserved mechanisms of biological functions, and the discovery of divergent functions served by conserved biological mechanisms.

What is this Documentation?

This documentation provides an introduction to the system and ways of working with it, explanations of core concepts, tutorials of general utility, as well as detailed reference documentation for the various components and processes that make up the system.