title: H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.
abstract: We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs. 'Navigation search' is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility.
authors.affiliation: BIRC, NIG Waterfront Bio-IT Research Building, 4-7 Aomi, Tokyo 135-0064, Japan.
authors.forename: Chisato
authors.initials: C
authors.lastname: Yamasaki
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Murakami
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Takeda
authors.forename: Yoshiharu
authors.initials: Y
authors.lastname: Sato
authors.forename: Akiko
authors.initials: A
authors.lastname: Noda
authors.forename: Ryuichi
authors.initials: R
authors.lastname: Sakate
authors.forename: Takuya
authors.initials: T
authors.lastname: Habara
authors.forename: Hajime
authors.initials: H
authors.lastname: Nakaoka
authors.forename: Fusano
authors.initials: F
authors.lastname: Todokoro
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsuya
authors.forename: Tadashi
authors.initials: T
authors.lastname: Imanishi
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
mesh_terms: D019295:Computational Biology / Q000379:methods* / Q000639:trends; D018076:DNA, Complementary / Q000378:metabolism; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D015894:Genome, Human; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008957:Models, Genetic; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger