PhenoFam

PhenoFam performs gene set enrichment analysis by integrating structural and functional annotations derived from protein domain families to identify domain-associated signals in high-throughput datasets such as gene expression microarrays and RNA interference screens.

Key Features:

• Integration of Structural and Functional Annotations: Combines protein domain structural features with functional roles to enable domain-centric GSEA.
• Comprehensive Dataset Analysis: Analyzes entire high-throughput datasets without requiring pre-filtering or selection of hits.
• Use of Ensembl and InterPro: Maps user-provided gene identifiers to protein features using the Ensembl and InterPro databases.

Scientific Applications:

• Discovery of Novel Gene Functions: Analysis of genome-wide RNA interference screens has identified new roles for genes, for example uncovering a previously unrecognized function of plexins containing the cytoplasmic RasGAP domain.
• Linkage to Disease Pathways: Analysis of breast cancer gene expression profiles revealed associations between altered expression of PX domain-containing proteins and breast carcinoma.

Methodology:

PhenoFam employs a methodological framework that assesses whether the results associated with specific protein domains significantly deviate from the overall population.