WormEnrichr is a new gene list enrichment analysis tool for Caenorhabditis elegans. WormEnrichr is derived from Enrichr, the popular web-based software for comprehensive and intuitive gene list enrichment analysis. Data from a variety of publicly available C. elegans databases was processed and integrated to generate a collection of gene set libraries. WormEnrichr can be accessed via API which are documented in SmartAPI. This makes WormEnrichr interoperable with other tools and projects.
The initial version of WormEnrichr contain the following new gene set libraries:
- Gene Ontology: The GO libraries were created using the core ontology from the Gene Ontology Consortium, annotated with associated C. elegans genes. A cross-section of the ontology tree was taken to create moderately sized gene sets. The three gene set libraries in WormEnrichr are: GO Biological Process, GO Cellular Component, and GO Molecular Function.
- WikiPathways: The WikiPathways library consists of all pathways for C. elegans in WikiPathways converted to gene sets.
- TF2DNA: TF2DNA contains regulatory interactions that connect transcription factors and the genes these factors putatively regulate based on DNA binding site motifs.
- BioGrid: BioGrid is a repository for storing molecular interaction between cellular components. The libraries created from BioGrid consist of all worm gene-gene phenotypic interactions and protein-protein interactions. The two gene set libraries in WormEnrichr are: Gene Interaction Hubs BioGRID and PPI Hubs BioGRID.
- Wormbase: WormBase is a model organism database for C. elegans. The libraries created from WormBase consist of phenotypic, anatomic, and human disease annotations. The four gene set libraries in WormEnrichr are: Phenotypes WormBase 2018, RNAi Phenotypes Wormbase 2018, Anatomic Associations WormBase 2018, and Human Diseases from WormBase 2018.