danRerLib

danRerLib provides a suite of tools for zebrafish transcriptomics including gene ID mapping, orthology mapping for zebrafish and human taxonomy, and functional enrichment analysis utilizing human-annotated functional annotations to overcome limitations in zebrafish-specific data.

Key Features:

• Gene ID mapping: Maps zebrafish gene identifiers between different database formats.
• Orthology mapping: Maps orthologs between zebrafish and human taxonomy to leverage cross-species functional annotations.
• Functional enrichment analysis: Performs enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, including pathways lacking direct zebrafish annotations through orthology with human-annotated functional annotations.

Scientific Applications:

• Functional enrichment of zebrafish transcriptomics data: Extends analysis to a wider range of GO and KEGG pathways by utilizing human ortholog annotations when zebrafish annotations are incomplete.
• Cross-species pathway analysis: Enables researchers to elucidate additional mechanisms and gain greater insight into experimental results by leveraging the closely mirrored zebrafish and human transcriptomes.

Methodology:

danRerLib utilizes orthology mapping between zebrafish and human taxonomy to enable functional enrichment analysis for GO and KEGG pathways that lack direct zebrafish annotations, leveraging human-annotated functional annotations through cross-species orthology.