FlyEnrichr is a new gene list enrichment analysis tool for Drosophila melanogaster. FlyEnrichr 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. melanogaster databases was processed and integrated to generate a collection of gene set libraries. FlyEnrichr can be accessed via API which are documented in SmartAPI. This makes FlyEnrichr interoperable with other tools and projects.
The initial version of FlyEnrichr 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. melanogaster genes. A cross-section of the ontology tree was taken to create moderately sized gene sets. The three gene set libraries in FlyEnrichr are: GO Biological Process, GO Cellular Component, and GO Molecular Function.
- WikiPathways: The WikiPathways library consists of all pathways for D. melanogaster 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.
- DroID: DroID is a comprehensive interactions database for D. melanogaster. The libraries created from DroID consist of protein-protein interactions, transcription factors and regulated genes, and putative targets of miRNAs. The three libraries in FlyEnrichr are: PPI Network Hubs DroID, Transcription Factors DroID, and Putative Regulatory miRNAs DroID.
- Human Disease Flybase: The library consists of fly models of human disease and the genes altered to produce the models.
- Allele Phenotypes FlyBase: The library consists of phenotypes and genes with known alleles that produce the phenotypes.
- Allele LoF Phenotypes FlyBase: The library consists of loss of function phenotypes and genes with known alleles that produce the phenotypes.
- Coexpression Predicted: Libraries were created using gene-gene expression correlations built from gene counts in GEO and SRA fly 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 FlyEnrichr are: Coexpression Predicted GO BP, Coexpression Predicted GO MF, and Coexpression Predicted GO CC.