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. 2008 Jan;36(Database issue):D793-9.
doi: 10.1093/nar/gkm999. Epub 2007 Dec 18.

The H-Invitational Database (H-InvDB), a Comprehensive Annotation Resource for Human Genes and Transcripts

Genome Information Integration Project And H-Invitational 2Chisato YamasakiKatsuhiko MurakamiYasuyuki FujiiYoshiharu SatoErimi HaradaJun-ichi TakedaTakayuki TaniyaRyuichi SakateShingo KikugawaMakoto ShimadaMotohiko TaninoKanako O KoyanagiRoberto A BarreroCraig GoughHong-Woo ChunTakuya HabaraHideki HanaokaYosuke HayakawaPhillip B HiltonYayoi KanekoMasako KannoYoshihiro KawaharaToshiyuki KawamuraAkihiro MatsuyaNaoki NagataKensaku NishikataAkiko Ogura NodaShin NurimotoNaomi SaichiHiroaki SakaiRyoko SanbonmatsuRie ShibaMami SuzukiKazuhiko TakabayashiAiko TakahashiTakuro TamuraMasayuki TanakaSusumu TanakaFusano TodokoroKaori YamaguchiNaoyuki YamamotoToshihisa OkidoJun MashimaAki HashizumeLihua JinKyung-Bum LeeYi-Chueh LinAsami NozakiKatsunaga SakaiMasahito TadaSatoru MiyazakiTakashi MakinoHajime OhyanagiNaoki OsatoNobuhiko TanakaYoshiyuki SuzukiKazuho IkeoNaruya SaitouHideaki SugawaraClaire O'DonovanTamara KulikovaEleanor WhitfieldBrian HalliganMary ShimoyamaSimon TwiggerKei YuraKouichi KimuraTomohiro YasudaTetsuo NishikawaYutaka AkiyamaChie MotonoYuri MukaiHideki NagasakiMakiko SuwaPaul HortonReiko KikunoOsamu OharaDoron LancetEric EvenoEsther GraudensSandrine ImbeaudMarie Anne DebilyYoshihide HayashizakiClara AmidMichael HanAndreas OsangerToshinori EndoMichael A ThomasMika HirakawaWojciech MakalowskiMitsuteru NakaoNam-Soon KimHyang-Sook YooSandro J De SouzaMaria de Fatima BonaldoYoshihito NiimuraVladimir KuryshevIngo SchuppStefan WiemannMatthew BellgardMasafumi ShionyuLibin JiaDanielle Thierry-MiegJean Thierry-MiegLukas WagnerQinghua ZhangMitiko GoShinsei MinoshimaMasafumi OhtsuboKousuke HanadaPeter TonellatoTakao IsogaiJi ZhangBoris LenhardSangsoo KimZhu ChenUrsula HinzAnne EstreicherKenta NakaiIzabela MakalowskaWinston HideNicola TiffinLaurens WilmingRanajit ChakrabortyMarcelo Bento SoaresMaria Luisa ChiusanoYutaka SuzukiCharles AuffrayYumi Yamaguchi-KabataTakeshi ItohTeruyoshi HishikiSatoshi FukuchiKen NishikawaSumio SuganoNobuo NomuraYoshio TatenoTadashi ImanishiTakashi Gojobori
Free PMC article

The H-Invitational Database (H-InvDB), a Comprehensive Annotation Resource for Human Genes and Transcripts

Genome Information Integration Project And H-Invitational 2 et al. Nucleic Acids Res. .
Free PMC article

Abstract

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

Figures

Figure 1.
Figure 1.
H-InvDB: overview of the comprehensive annotation resource for the human genes and transcripts. The current H-InvDB annotation resources consist of two main views, Transcript view and Locus view, and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group view. The Transcript view and the Locus view are the main viewers to display the annotation of each H-Invitational transcript (HIT) and H-Invitational cluster (HIX). The DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group view are sub-databases to provide detailed annotation for each annotation feature. The links to related databases are provided from the appropriate viewers.

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