gProfileR

gProfileR performs functional enrichment analysis, gene identifier conversion, and homologous gene mapping to interpret gene lists from high-throughput experiments.

Key Features:

• Functional Enrichment Analysis: Conducts enrichment on both flat and ranked gene lists to identify statistically significant Gene Ontology (GO) terms, biological pathways, and related functional annotations.
• Gene Identifier Conversion: Translates across hundreds of gene identifiers to enable interoperability between diverse datasets.
• Homologous Gene Mapping: Maps homologous genes across 213 organisms including mammals, other vertebrates, plants, insects, and fungi.
• Integration with Ensembl Database: Synchronizes data quarterly with Ensembl to incorporate current genome and pathway information.
• Expanded Functional Datasets (2016 update): Includes transcription factor binding site predictions, Mendelian disease annotations, protein expression and complex data, and gene mappings of human genetic polymorphisms.
• Programmatic Interfaces: Provides programmatic access via an R package, a Python interface, and a BioJS component for integration into computational workflows.

Scientific Applications:

• Annotation of high-throughput experiments: Interprets gene lists from RNA sequencing, ChIP-seq, and other genomic studies by linking genes to GO terms and pathways.
• Comparative genomics and evolutionary studies: Uses homolog mapping across 213 species to support cross-species analyses and evolutionary inference.
• Disease and variant interpretation: Leverages Mendelian disease annotations and human genetic polymorphism mappings to aid translational and clinical research.

Methodology:

Performs statistical enrichment analysis (over-representation) on flat and ranked gene lists to detect significant GO terms, pathways and other annotations; converts gene identifiers and maps homologs across species; relies on data synchronized quarterly from the Ensembl database and incorporates TFBS predictions, disease annotations, protein expression/complex data, and human polymorphism mappings.