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H-Invitational Database (H-InvDB) release 5.0 ,

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).

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H-Invitational Database (H-InvDB) release 5.0 ,

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  1. 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)

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

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

  4. SNP What is H-InvDB? Annotation categories • Gene structures • Gene functions • Relation with diseases • Evolutionary features • Protein 3D structure • Subcellular localization • Genetic polymorphism • Gene expression profilingetc Annotation of 187,156 transcripts, 36,073 gene clusters

  5. H-InvDB official page, Top page & Search tools www.h-invitational.jp H-InvDB Top page • Search tools • Text/keyword search • Advanced search • BLAST search • H-InvDB Navi

  6. H-InvDB views:2 main views and 8 sub-databases http://www.h-invitational.jp

  7. 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 related-information • Hyperlinks to other databases

  8. 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

  9. 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 Search window Notion ESTs RefSeq & Ensembl H-Inv transcript(Green) Genome (purple)

  10. 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.)

  11. 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)

  12. 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

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

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

  15. 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

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

  17. H-InvDB entry points #1 Simple search Enter keyword eg. BC003551 #7 H-InvDB Navi Navigation system #6 Blast search By sequence similarity #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

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

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

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

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

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

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

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

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

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

  27. H-InvDB documentation • About H-Invitational project • Help documents • 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 ?

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

  29. Thank you !!

  30. 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.

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