H-Invitational Database (H-InvDB) release 5.0, an integrated database of human genes and transcripts Released on 2007/12/26 Integrated database team Japan Biological Information Research Center (JBIRC) National Institute of Advanced Industrial Science and Technology (AIST)

International Collaborative Project “H-Invitational” Human full-length cDNAs were collected from 6 FLcDNA project World’s 44 institutes ， 118 scientists participated

Manually curated by scientists High-Quality Free public human gene database create database Annotated by uniform basis International Collaborative Project “H-Invitational”

Annotation of 187,156 transcripts, 36,073 gene clusters What is H-InvDB? 1.Gene structures 2.Gene functions 3.Relation with diseases 4.Evolutionary features 5.Protein 3D structure 6.Subcellular localization 7.Genetic polymorphism 8.Gene expression profiling etc SNP Annotation categories

H-InvDB official page, Top page & Search tools H-InvDB Top page Search tools 1.Text/keyword search 2.Advanced search 3.BLAST search 4.H-InvDB Navi

H-InvDB views :2 main views and 8 sub-databases

H-InvDB: main viewers (1) H-InvDB: main viewers (1) Locus View Locus View  36,073 predicted genetic loci annotations  Gene structures  Alternative splicing isoforms  Gene expression profiles  cDNA/ORF multiple alignments  Disease related- information  Hyperlinks to other databases

H-InvDB: main viewers (2) H-InvDB: main viewers (2) Transcript view  187,156 transcripts annotations  Protein functions  Location on the chromosome  Open reading frame  InterPro motif  Evolutionary feature  Secondary/tertiary structure  Subcellar Localization  SNPs/microsatellites  hyperlinks to other databases

H-InvDB: sub-database(1) H-InvDB: sub-database(1)G-integra  Genome map browser  Structure of gene cluster  Mapping Info. with all EST, ens_gene and ref_gene by UCSC  Orthologous genes of other species  Repeat, SNPs, microsatellite, ACC#, ID search  Hyperlinks to other databases  Gene structures for 11 species; Mouse, Rat, Chimpanzee, etc H-Inv transcript(Green) RefSeq & Ensembl Genome (purple) ESTs Notion Search window

H-Inv DB: sub-database(2) H-Inv DB: sub-database(2) Human ANatomic Gene Expression Library (H-ANGEL)  Gene expression Library  Pattern Similarity Search  10 and 40 categories of organs and tissues  Analyzed by several platforms (iAFLP, SAGE and DNA array etc.)

H-Inv DB: sub-database(3) H-Inv DB: sub-database (3) DiseaseInfo Viewer  Database of known and orphan genetic diseases  H-Inv loci with LocusLink, OMIM and GenAtlas  Known disease-related gene  Co-localized orphan pathology (candidate gene is unknown)  Database of known and orphan genetic diseases  H-Inv loci with LocusLink, OMIM and GenAtlas  Known disease-related gene  Co-localized orphan pathology (candidate gene is unknown)

H-Inv DB: sub-database(4, 5) H-Inv DB: sub-database (4, 5) Clustering Viewer & TOPO viewer Clustering Viewer TOPO Viewer  A viewer for making comparison between different methods  Mapping-based & cDNA-based clustering  A Tool for viewing subcellular localization  Subcellular targeting signals were predicted by PSORT II and TargetP  Transmembrane helices were predicted by SOSUI and TMHMM

Evolutionary annotation database Human-curated orthologs Phylogenic trees Multiple alignment Search database Evolutionary annotation database Human-curated orthologs Phylogenic trees Multiple alignment Search database H-Inv DB: sub-database(6) H-Inv DB: sub-database(6)Evola

Database of human protein-protein interaction (PPI) H-Inv DB: sub-database (7) H-Inv DB: sub-database (7) PPI view

H-Inv DB: sub-database (8) H-Inv DB: sub-database (8) Gene Families/Groups * H-InvDB Gene Families/Groups Detailed annotations for the four selected gene families/groups. 1. T-cell receptor (TCR) Gene symbols: TRBC1, TRAC, 2. Immunoglobulin (Ig) Gene symbols: IGKC, IGHA1, IGHE, IGHG1 IGHM, IGLC1, etcIGKCIGHG1 3. Major histocompatibility complex (MHC) or human leukocyte antigen (HLA) Gene symbols: HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-E, HLA-F, HLA-G, etc 4. Olfactory receptors (OR) Gene symbols: OR1C1, OR2C3, OR3A1, OR4C6, OR5F1, OR6A2, OR7A5, OR8A1, OR9Q1, etc

Applications of H-InvDB 1.H-InvDB entry points to annotated data 2.H-InvDB application#1 “If you look for gene of certain feature” 3.H-InvDB application#2 If you sequenced a new gene “If you sequenced a new gene” 4.H-InvDB annotation data download 5.Documentation 6.Contact to H-InvDB

H-InvDB entry points #1 Simple search Enter keyword eg. BC #3 Chromosome Map Jump to genome map #2 Advanced search For detailed search #6 Blast search By sequence similarity #5 Sample views Jump to each sample view #7 H-InvDB Navi Navigation system #4 Site map Jump to each sample view

H-InvDB Application#1-1 H-InvDB Application#1-1 “Genes of certain feature” Recommended entry points: 1.Search by simple search 2.Search by advanced search 3.H-InvDB Navi Enter keyword e.g. kinase List of H-InvDB entries of a certain feature H-InvDB top page Links to each H-Inv cDNA & Locus view

H-InvDB Application#1-2 H-InvDB Application#1-2 “Genes of certain feature” Recommended entry points: 1.Search by simple search 2.Search by advanced search 3.H-InvDB Navi Link to Advanced search H-InvDB top page Select search items & enter IDs or keywords Select dataset Advanced search

Recommended entry points: 1.Search by simple search 2.Search by advanced search 3.H-InvDB Navi Link to H-InvDB Navi H-InvDB top page Select search items H-InvDB Application#1-3 H-InvDB Application#1-3 “Genes of certain feature” H-InvDB Navi

Recommended entry points: –Blast sequence similarity search Link to BLAST H-InvDB top page Enter sequence and “Search” H-InvDB Application#2 “New sequence” Blast search

H-InvDB annotation data format 3 annotation data formats JBIRC flat file format DDBJ flat file format JBIRC XML file format

H-InvDB data download sites 2 data download sites 1.HTTP site 2.FTP site Jump to Download H-InvDB top page HTTP download site Downloading annotated data

H-InvDB data download page 2 data download site 1.HTTP site 2.FTP site Jump to FTP server H-InvDB official page Downloading annotated data FTP download site

H-InvDB annotation data download Data download from each view 1.JBIRC flat file format 2.JBIRC XML format 3.DDBJ format 4.Sequence FASTA files Click on each icon to download annotation data Transcript view

H-InvDB annotation data download Data download from each view 1.JBIRC flat file format 2.JBIRC XML format 3.DDBJ format 4.Sequence FASTA files Transcript view Select at pull-down menu and click on “Download”

H-InvDB documentation 1.About H-Invitational project 2.Help documents 1.What is H-InvDB ? 2.Annotation policies 3.Search usage 4.Viewer manuals 5.Flat file format 6.FAQ 7.How to site H-InvDB Help 1. What is H-InvDB ?

Contact to H-InvDB Please contact us for any question or comments !! 1.Click on “Contact us” in any H-InvDB view 2.Fill the form 3.Click on “Submit”

Thank you !!

Acknowledgements Members of the H-Invitational Consortium. The providers of the human full-length cDNAs (DKFZ, MGC/NIH, CHGC, IMSUT, KDRI, HRI and FLJ of NEDO) All Staffs of JBIRC This project was supported in part by grants from METI, MEXT, JBIC, NEDO, DOE, NIH, BMBF, EU, CNRS, AIST and NIG.