GFINDer

GFINDer annotates and statistically analyzes gene lists to associate genes with OMIM clinical phenotypes and diverse functional categories for interpretation of microarray and genetic disorder studies.

Key Features:

• Phenotype Analysis: Maps genes to the Online Mendelian Inheritance in Man (OMIM) database, normalizes phenotype location descriptions into unique controlled terms, and structures phenotypes and diseases hierarchically for automatic annotation of gene lists.
• Gene Classification: Classifies genes according to genetic syndromes and phenotypic location categories and identifies statistically significant phenotype location categories within each gene class.
• Functional Annotation and Analysis: Retrieves annotations from multiple databases across various functional categories, identifies enriched categories within user-classified gene lists, and computes statistical significance values for those enrichments.
• Statistical Evaluation: Evaluates the relevance of annotations, estimates functional bias introduced by gene sets identified from high-density microarray experiments, and performs statistical analyses on classifications to aid biological interpretation.

Scientific Applications:

• Genetic Disorder Research: Analysis of genes related to inherited diseases using OMIM-derived clinical phenotypes to support studies of the genetic basis of disorders.
• Gene Expression Studies: Interpretation of gene expression results (e.g., high-density microarray-derived gene lists) by providing functional profiles and statistically enriched annotations to elucidate pathophysiological mechanisms.

Methodology:

Hierarchical structuring of phenotype and disease data from OMIM, integration of annotations from multiple databases, and application of statistical analyses to assess annotation relevance and functional bias.