Abstract
AbstractH-Invitational Database (H-InvDB: "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in 46,499 human gene clusters based on human full-length cDNAs, mRNAs and the reference human genome sequences (NCBI b37.1). H-InvDB consists of three main views, the Transcript view, the Locus view and the Protein view, and six sub-databases; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view. We also provide data mining tools such as “Navigation search”, an extended search system that enables complicated searches by combining 16 different search options ("http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp":http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp) and “H-InvDB Enrichment Analysis Tool (HEAT)”, a data mining tool for automatically identifying features specific to a given human gene set ("http://hinv.jp/HEAT/":http://hinv.jp/HEAT/).
Highlights
Chisato Yamasaki1, Jun-ichi Takeda1, Takuya Habara1, Makoto Ogawa2,3, Akiko Noda1, Ryuichi Sakate1, Katsuhiko Murakami2, Tadashi Imanishi1 and Takashi Gojobori1,4
H-InvDB_1.0 was released 2004/04/20 Provided by BIRC/AIST and DDBJ, Japan
# H-InvDB web service provide SOAP and REST APIs. # System designed on the standard web-service guideline proposed in “Odaiba Manifesto”
Summary
H-InvDB_1.0 was released 2004/04/20 Provided by BIRC/AIST and DDBJ, Japan. - Re-difinition of human gene clusters on NCBI b37.1 (UCSC hg19) by re-filtering the predicted gene models - 242,813 human transcripts in 44,806 human gene clusters (loci). - Improvement on alternative splicing annotation pipeline and update of H-DBAS - Update in human protein-protein interaction (PPI) and update of PPI view - Updates of subdatabases; G-integra, DiseaseInfo Viewer, H-ANGEL, Gene family/groups - Re-difinition of human gene clusters on NCBI b37.1 (UCSC hg19) by re-filtering the predicted gene models - 242,813 human transcripts in 44,806 human gene clusters (loci). - Improvement on alternative splicing annotation pipeline and update of H-DBAS - Update in human protein-protein interaction (PPI) and update of PPI view - Updates of subdatabases; G-integra, DiseaseInfo Viewer, H-ANGEL, Gene family/groups
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