H-InvDB

H-InvDB provides comprehensive annotations of human genes and transcripts for genetic and functional genomics research (version 6.2: 219,765 transcripts organized into 43,159 gene clusters) derived from full-length cDNAs and mRNAs.

Key Features:

• Gene structures: Detailed annotation of exon–intron organization and gene models.
• Alternative splicing isoforms: Annotation and cataloguing of transcript isoforms produced by alternative splicing.
• Non-coding RNAs (ncRNAs): Annotation of non-coding functional RNAs and relationships to known ncRNAs.
• Protein functions: Functional annotation of encoded proteins based on sequence and database evidence.
• Functional domains: Identification and annotation of protein functional domains.
• Sub-cellular localization: Annotation of predicted or known protein sub-cellular localizations.
• Metabolic pathways: Assignment of proteins to metabolic pathways.
• Three-dimensional protein structures: Links or annotations related to 3D protein structure information.
• Genetic polymorphisms: Annotation of single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and microsatellite repeats.
• Disease associations: Annotation of gene and transcript associations with human diseases.
• Gene expression profiles: Inclusion of expression profile annotations for transcripts and genes.
• Molecular evolutionary features: Annotation of evolutionary characteristics of genes and proteins.
• Protein–protein interactions: Annotation of known or inferred protein–protein interactions.
• Gene families/groups: Classification of genes into families and groups.
• Microarray probe mapping: Mapping of microarray probes to transcripts and gene models.
• Updated gene models: Inclusion of revised and updated gene model annotations.
• Glycogene integration: Inclusion of data from the Glycogene database.
• Navigation search: Query capability combining up to 16 options for complex retrieval criteria.
• H-InvDB Enrichment Analysis Tool (HEAT): Detection of annotations significantly enriched in user-defined gene sets compared with the entire database of representative transcripts.
• Web service APIs: Programmatic access via SOAP and REST web service interfaces.

Scientific Applications:

• Gene model curation: Refinement and validation of exon–intron structures and transcript models.
• Alternative splicing analysis: Study of transcript isoform diversity and splicing patterns.
• ncRNA characterization: Identification and characterization of non-coding functional RNAs and their relationships to genes.
• Protein function and domain analysis: Functional annotation and domain-based analyses of protein products.
• Sub-cellular localization studies: Investigation of protein localization in cellular compartments.
• Pathway reconstruction: Assignment of genes and proteins to metabolic and signaling pathways.
• Structural biology integration: Linking transcript/ protein annotations to three-dimensional structure data.
• Genetic variation and disease association studies: Analysis of SNPs, indels, microsatellites and their associations with disease.
• Expression profiling: Interpretation and re-annotation of gene expression datasets, including microarray probe mapping.
• Evolutionary and comparative genomics: Analyses of molecular evolutionary features across gene families.
• Protein–protein interaction analysis: Exploration of interaction networks informed by annotated interactions.
• Gene set enrichment analysis: Identification of annotations enriched in user-defined gene lists using HEAT.
• Programmatic integration: Integration of H-InvDB data into computational workflows via SOAP and REST APIs.

Methodology:

Annotations are derived from full-length cDNAs and mRNAs; gene models are updated and microarray probes are mapped; relationships to known ncRNAs and Glycogene database data are integrated; HEAT detects annotations significantly enriched in user-defined gene sets relative to the database of representative transcripts; web service APIs are implemented using SOAP and REST.