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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 International Collaborative Project “H-Invitational” Manually curated by scientists Annotated by uniform basis create database High-Quality Free public human gene database What is H-InvDB? Annotation categories 1. 2. 3. 4. 5. 6. 7. 8. Gene structures Gene functions Relation with diseases Evolutionary features Protein 3D structure Subcellular localization Genetic polymorphism Gene expression profiling etc SNP Annotation of 187,156 transcripts, 36,073 gene clusters H-InvDB official page, Top page & Search tools www.h-invitational.jp Search tools 1. Text/keyword search 2. Advanced search 3. BLAST search 4. H-InvDB Navi H-InvDB Top page H-InvDB views :2 main views and 8 sub-databases http://www.h-invitational.jp H-InvDB: main viewers (1) Locus View 36,073 predicted genetic loci annotations Gene structures Alternative splicing isoforms Gene expression profiles cDNA/ORF multiple alignments Disease relatedinformation Hyperlinks to other databases 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) G-integra Search window Notion ESTs RefSeq & Ensembl H-Inv transcript(Green) Genome (purple) 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 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) 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) H-Inv DB: sub-database (4, 5) Clustering Viewer & TOPO viewer Clustering Viewer A viewer for making comparison between different methods Mapping-based & cDNA-based clustering TOPO Viewer A Tool for viewing subcellular localization Subcellular targeting signals were predicted by PSORT II and TargetP Transmembrane helices were predicted by SOSUI and TMHMM H-Inv DB: sub-database(6) Evola Evolutionary annotation database Human-curated orthologs Phylogenic trees Multiple alignment Search database H-Inv DB: sub-database (7) PPI view Database of human protein-protein interaction (PPI) 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, TRD@ 2. Immunoglobulin (Ig) Gene symbols: IGKC, IGHA1, IGHE, IGHG1 IGHM, IGHV@, IGLC1, etc 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” 4. H-InvDB annotation data download 5. Documentation 6. Contact to H-InvDB H-InvDB entry points #7 H-InvDB Navi #6 Blast search Navigation system By sequence similarity #1 Simple search Enter keyword eg. BC003551 #2 Advanced search For detailed search #3 Chromosome Map Jump to genome map #4 Site map Jump to each sample view #5 Sample views Jump to each sample view H-InvDB Application#1-1 “Genes of certain feature” • Recommended entry points: 1. Search by simple search 2. 3. Search by advanced search H-InvDB Navi H-InvDB top page Enter keyword e.g. kinase List of H-InvDB entries of a certain feature Links to each H-Inv cDNA & Locus view 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 H-InvDB top page Link to Advanced search Advanced search Select dataset Select search items & enter IDs or keywords H-InvDB Application#1-3 “Genes of certain feature” • Recommended entry points: 1. 2. Search by simple search Search by advanced search 3. H-InvDB Navi H-InvDB top page Link to H-InvDB Navi H-InvDB Navi Select search items H-InvDB Application#2 “New sequence” • Recommended entry points: – Blast sequence similarity search H-InvDB top page Link to BLAST Blast search Enter sequence and “Search” H-InvDB annotation data format • 3 annotation data formats JBIRC XML file format JBIRC flat file format DDBJ flat file format H-InvDB data download sites • 2 data download sites 1. HTTP site 2. HTTP download site FTP site H-InvDB top page Jump to Download Downloading annotated data H-InvDB data download page • 2 data download site 1. HTTP site FTP download site 2. FTP site H-InvDB official page Downloading annotated data Jump to FTP server H-InvDB annotation data download • Data download from each view 1. 2. 3. 4. JBIRC flat file format JBIRC XML format DDBJ format Sequence FASTA files Transcript view Click on each icon to download annotation data H-InvDB annotation data download • Data download from each view 1. 2. 3. 4. JBIRC flat file format JBIRC XML format DDBJ format Sequence FASTA files Select at pull-down menu and click on “Download” Transcript view H-InvDB documentation 1. About H-Invitational project 2. Help documents 1. 2. 3. 4. 5. 6. 7. What is H-InvDB ? Annotation policies Search usage Viewer manuals Flat file format FAQ 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.