1 / 30

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).

edolie
Download Presentation

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

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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.

More Related