modEnrichr

modEnrichr extends the Enrichr platform to perform gene set enrichment analysis for model organisms (fish, fly, worm, yeast) by providing organism-specific gene set libraries, RNA-seq co-expression–based function prediction, and ortholog conversion for cross-species analysis.

Key Features:

• Expanded Gene Set Libraries: Each organism module (FishEnrichr, FlyEnrichr, WormEnrichr, YeastEnrichr) contains curated gene sets compiled from Gene Ontology, mRNA expression profiles, GeneRIF annotations, pathway databases, protein domain databases, and organism-specific resources.
• Data Integration into Gene Sets: Experimental results are abstracted into gene sets to enable integration across diverse datasets.
• Ortholog Conversion Tool: Automatically detects the species from input gene lists and converts orthologs to enable cross-species analyses.
• RNA-seq Co-expression Libraries: Predicts gene function from RNA-seq co-expression data uniformly processed from the Gene Expression Omnibus (GEO) for each organism.
• API Batch Access: Provides an API that supports batch queries for programmatic enrichment analyses.

Scientific Applications:

• Functional Genomics: Enables functional annotation and hypothesis generation from gene lists using organism-specific libraries and co-expression predictions.
• Pathway Analysis: Facilitates pathway-level interpretation using pathway databases included in the gene sets.
• Comparative Biology: Supports ortholog-based cross-species comparisons and comparative studies across fish, fly, worm, and yeast.
• Cross-species Hypothesis Generation: Enables generation of cross-species hypotheses by integrating co-expression predictions and ortholog conversion.

Methodology:

Experimental results are abstracted into gene sets; libraries are compiled from Gene Ontology, mRNA expression profiles, GeneRIF, pathway and protein domain databases, and organism-specific resources; gene function is predicted from RNA-seq co-expression data uniformly processed from GEO; species are automatically detected from gene lists for ortholog conversion; an API supports batch queries.