FishEnrichr is a new gene list enrichment analysis tool for Danio rerio. FishEnrichr is derived from Enrichr, the popular web-based software for comprehensive and intuitive gene list enrichment analysis. Data from a variety of publicly available D. rerio databases was processed and integrated to generate a collection of gene set libraries. FishEnrichr can be accessed via API which are documented in SmartAPI. This makes FishEnrichr interoperable with other tools and projects.
The initial version of FishEnrichr 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 D. rerio genes. A cross-section of the ontology tree was taken to create moderately sized gene sets. The three gene set libraries in FishEnrichr are: GO Biological Process, GO Cellular Component, and GO Molecular Function.
- WikiPathways: The WikiPathways library consists of all pathways for D. rerio in WikiPathways converted to gene sets.
- Coexpression Predicted: Libraries were created using gene-gene expression correlations built from gene counts in GEO and SRA fish experiments, based on a methodology developed in ARCHS4. The average correlation of a gene to all the genes currently associated with a term is calculated, scaled using zscore, and the top 200 genes with scores greater than 1.95 are predicted to be associated with the term. The three libraries in FishEnrichr are: Coexpression Predicted GO BP, Coexpression Predicted GO MF, and Coexpression Predicted GO CC.