Onto-Tools

Onto-Tools provides integrated functional annotation, Gene Ontology (GO)-based profiling, KEGG pathway analysis, identifier mapping, and codon-substitution analysis for genomic and gene expression datasets.

Key Features:

• Annotation Database: Expanded annotation database incorporating genomic data from over 19 sequence, gene, protein, and annotation databases with complete GO annotations and additional data for Rattus norvegicus, Drosophila melanogaster, and Caenorhabditis elegans.
• Onto-Express (OE): Translates lists of differentially regulated genes into GO-based functional profiles across categories including biochemical function, biological process, cellular role, molecular function, and chromosome location, supporting 24 organisms and various input IDs with statistical significance values.
• Onto-Compare (OC): Compares functional biases among over 170 commercial microarrays to aid array selection based on biological processes or pathways.
• Onto-Design (OD): Enables experiment design by keyword specification when exact GO terms are unknown and includes an integrated GO browser for customizable abstraction levels.
• Onto-Translate (OT): Performs non-redundant identifier mapping across 29 types of IDs and 53 organisms using the Onto-Tools database.
• Onto-Miner (OM): Provides unified programmatic access (API) to the majority of available annotations in the Onto-Tools database.
• Pathway-Express: Identifies significant pathways for input gene lists by integrating data from the KEGG pathway database.
• Promoter-Express: Identifies transcription factor binding sites active under specific conditions.
• nsSNPCounter: Computes and analyzes synonymous and non-synonymous codon substitutions to study evolutionary rates in protein-coding genes.

Scientific Applications:

• Functional profiling of differential expression: Translating microarray or gene expression lists into GO functional profiles to interpret biological roles of regulated genes.
• Pathway enrichment and identification: Detecting significantly impacted pathways by integrating gene lists with the KEGG pathway database via Pathway-Express.
• Microarray comparison and selection: Assessing functional biases across over 170 commercial microarrays to inform array choice for specific biological processes or pathways.
• Identifier integration and data consolidation: Mapping across 29 ID types and 53 organisms to integrate heterogeneous genomic datasets and annotations.
• Evolutionary rate analysis: Estimating synonymous and non-synonymous substitution patterns in protein-coding genes using nsSNPCounter.
• Experimental design support: Designing experiments through keyword-based selection of GO terms and a GO browser for adjustable abstraction levels.

Methodology:

Employs Gene Ontology Consortium nomenclature to standardize annotations. Calculates statistical significance values for GO categories. Integrates the KEGG pathway database for pathway identification. Computes synonymous and non-synonymous codon substitutions. Performs non-redundant ID mapping across 29 ID types and 53 organisms. Provides an application programming interface to access annotations and a GO browser for customizable abstraction levels.