GoSurfer

GoSurfer visualizes and analyzes associations between gene lists and Gene Ontology (GO) terms to identify and explore enriched biological processes, molecular functions, and cellular components.

Key Features:

• Input Flexibility: Accepts one or two lists of gene identifiers, including Affymetrix probe set IDs, from microarrays and other high-throughput experiments.
• Gene Ontology Association: Retrieves all associated Gene Ontology (GO) terms for input genes across biological process, molecular function, and cellular component ontologies.
• Hierarchical Visualization: Constructs and displays GO terms as a hierarchical tree to represent relationships among GO terms.
• Statistical Analysis Integration: Performs enrichment tests on GO term associations and highlights significantly enriched GO terms within the GO hierarchy.
• Interactive Exploration: Supports manipulation of the GO hierarchy via heuristic thresholds and statistical filters and enables querying of genes associated with specific GO terms.
• Data Export Options: Exports GO-related results as text files and saves visualizations as graphic files.

Scientific Applications:

• Microarray and high-throughput data analysis: Maps gene sets from microarray experiments and other parallel high-throughput methods to GO terms for functional interpretation.
• Functional enrichment and hypothesis generation: Identifies enriched GO terms to support hypothesis generation and validation in gene regulation and functional genomics studies.
• Interpretation of expression patterns: Aids interpretation of the physiological implications of complex gene expression patterns through GO-term enrichment.

Methodology:

Retrieves GO annotations for input gene identifiers (including Affymetrix probe set IDs), maps genes to GO terms, builds a hierarchical GO tree, applies enrichment tests with heuristic thresholds or statistical filters, enables querying of gene–GO associations, and exports results as text and graphic files.