The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• The H-Invitational Database (H-InvDB) is a crucial resource for human transcriptome annotation.
• Previous versions focused on full-length cDNA (FLcDNA) annotation.
• Continuous updates are necessary to incorporate new sequence data and improve annotation quality.

Purpose of the Study:

• To report new features and improvements in the latest release of H-InvDB (version 4.6).
• To provide comprehensive annotation for a larger set of human mRNAs and FLcDNAs.
• To enhance the utility of H-InvDB as a resource for human gene and transcript research.

Main Methods:

• Annotation of 120,558 human mRNAs from International Nucleotide Sequence Databases (INSD) and 54,978 human FLcDNAs.
• Mapping transcripts to human genome sequences (NCBI build 36.1) to define gene clusters.
• Comprehensive annotation including gene structures, functions, splicing variants, ncRNAs, pathways, protein structures, SNPs, and disease associations.

Main Results:

• H-InvDB_4.6 annotates 175,536 human transcripts, defining 34,699 gene clusters (34,057 protein-coding, 642 non-protein-coding).
• 2.5% of transcribed loci overlap with predicted pseudogenes.
• Extensive annotation data includes functional domains, subcellular localization, metabolic pathways, protein 3D structure predictions, SNP mapping, disease co-localization, and gene expression profiles.

Conclusions:

• H-InvDB_4.6 represents a significant expansion and improvement of the human transcriptome annotation resource.
• The database provides integrated views (Transcript and Locus) and specialized sub-databases for diverse research needs.
• This updated resource facilitates deeper understanding of human genes, transcripts, and their functions, including disease associations and protein-protein interactions.