Affymetrix NetAffx Analysis Center

Affymetrix NetAffx Analysis Center provides probeset- and sequence-level annotations and cross-references for Affymetrix GeneChip microarrays to support interpretation of gene expression data.

Key Features:

• Probeset Annotation: Detailed annotations for each GeneChip probeset including static information on probeset composition.
• Sequence Annotations: Sequence annotations extracted from public databases and protein-level annotations derived from public-domain programs and proprietary hidden Markov model (HMM) libraries.
• Interactive Maps and Contextual Data: Genomic maps that display sequence data within a genomic context for larger chip sets.
• Gene Ontology (GO) Integration: Inclusion of Gene Ontology terms and graphical representations of GO relationships.
• Protein Domains and Motifs: Predicted protein domains and motifs associated with arrayed sequences.
• Orthologous Sequences and Pathways: Links to orthologous sequences and relevant biological pathways to support comparative and pathway analyses.
• Database Connectivity: Direct links to public databases including UniGene, LocusLink (now part of NCBI), SWISS-PROT, and OMIM.

Scientific Applications:

• Genomics, Transcriptomics, Proteomics: Correlating GeneChip expression results with detailed annotations to support analyses across genomics, transcriptomics, and proteomics.
• Gene Expression Analysis: Enabling comprehensive interpretation of gene expression experiments using probeset and sequence-level annotations.
• Gene and Pathway Discovery: Identifying novel genes or pathways involved in biological processes or diseases through annotated array results.
• Cross-Reference Validation: Validating array-derived findings by cross-referencing with established databases and annotations.

Methodology:

Integration of static probeset composition information with dynamic sequence annotations extracted from public databases and generation of protein-level annotations using public-domain programs and proprietary HMM libraries.