H-Invitational Database (H-InvDB) release 5.0 ,
description
Transcript of H-Invitational Database (H-InvDB) release 5.0 ,
H-Invitational Database (H-InvDB) release H-Invitational Database (H-InvDB) release 5.05.0, ,
an integrated database of human genes and an integrated database of human genes and transcriptstranscripts
Released on 2007/12/26Released on 2007/12/26Integrated database team
Japan Biological Information Research Center (JBIRC)National Institute of Advanced Industrial Science and Technology (AIST)
International Collaborative Project International Collaborative Project ““H-Invitational”H-Invitational”
Human full-length cDNAs were collected from 6 FLcDNA project
World’s 44 institutes, 118 scientists participated
Manually curated by scientists Manually curated by scientists
High-QualityFree public human gene
database
create database
Annotated by uniform basis
International Collaborative Project International Collaborative Project ““H-Invitational”H-Invitational”
Annotation of 187,156 transcripts, 36,073 gene clusters
What is H-What is H-InvDB?InvDB?
1. Gene structures2. Gene functions3. Relation with diseases4. Evolutionary features5. Protein 3D structure6. Subcellular localization7. Genetic polymorphism8. Gene expression profiling etc
SNP
Annotation categories
H-InvDB official page, H-InvDB official page, Top page & Search tools Top page & Search tools
H-InvDB Top page
Search tools1. Text/keyword search2. Advanced search3. BLAST search4. H-InvDB Navi
www.h-invitational.jp
H-InvDB viewsH-InvDB views :2 main views and 8 sub-databases:2 main views and 8 sub-databases
http://www.h-invitational.jphttp://www.h-invitational.jp
H-InvDB: main viewers (1)H-InvDB: main viewers (1) Locus View Locus View
36,073 predicted 36,073 predicted genetic loci genetic loci annotationsannotations
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 viewTranscript view
187,156 transcripts annotatio187,156 transcripts annotationsns
Protein functions Location on the chromosome Open reading frame InterPro motif Evolutionary feature Secondary/tertiary structure Subcellar Localization SNPs/microsatellites hyperlinks to other database
s
H-InvDB: sub-database(1)H-InvDB: sub-database(1)G-integraG-integra
Genome map browserGenome map browser Structure of gene cluster Mapping Info. with all EST, en
s_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 speciGene structures for 11 speci
es; Mouse, Rat, Chimpanzees; Mouse, Rat, Chimpanzee, etce, etc
H-Inv transcript(Green)H-Inv transcript(Green)
RefSeq & EnsemblRefSeq & Ensembl
Genome (purple)Genome (purple)
ESTsESTs NotionNotion
Search windowSearch window
H-Inv DB: sub-database(2)H-Inv DB: sub-database(2)Human ANatomic Gene Expression Library (H-ANGEL)Human ANatomic Gene Expression Library (H-ANGEL)
Gene expression Library 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-databaseH-Inv DB: sub-database (3)(3)DiseaseInfo ViewerDiseaseInfo Viewer
Database of known and orDatabase of known and orphan genetic diseases phan genetic diseases
H-Inv loci with LocusLink, OMIM and GenAtlas
Known disease-related gene Co-localized orphan patholo
gy (candidate gene is unknown)
Database of known and orDatabase of known and orphan genetic diseases phan genetic diseases
H-Inv loci with LocusLink, OMIM and GenAtlas
Known disease-related gene Co-localized orphan patholo
gy (candidate gene is unknown)
H-Inv DB: sub-databaseH-Inv DB: sub-database (4, 5)(4, 5)Clustering Viewer & TOPO viewerClustering Viewer & TOPO viewer
Clustering ViewerClustering Viewer
TOPO ViewerTOPO Viewer
A viewer for making A viewer for making comparison between different comparison between different methodsmethods
Mapping-based & cDNA-based Mapping-based & cDNA-based clusteringclustering
A Tool for viewing subcellular A Tool for viewing subcellular localizationlocalization
Subcellular targeting signals were Subcellular targeting signals were predicted by PSORT II and TargetPpredicted by PSORT II and TargetP
Transmembrane helices were predicted Transmembrane helices were predicted by SOSUI and TMHMMby SOSUI and TMHMM
Evolutionary annotation Evolutionary annotation databasedatabase
Human-curated orthologs Phylogenic trees Multiple alignment Search database
Evolutionary annotation Evolutionary annotation databasedatabase
Human-curated orthologs Phylogenic trees Multiple alignment Search database
H-Inv DB: sub-database(6)H-Inv DB: sub-database(6)EvolaEvola
Database of human protein-protein interaction (PPI)
Database of human protein-protein interaction (PPI)
H-Inv DB: sub-database (7)H-Inv DB: sub-database (7)PPI viewPPI 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, 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-InvDBApplications of H-InvDB1. 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 geneIf you sequenced a new gene”
4. H-InvDB annotation data download
5. Documentation
6. Contact to H-InvDB
H-InvDB entry pointsH-InvDB entry points#1 Simple search
Enter keywordeg. BC003551
#3 Chromosome MapJump to genome map
#2 Advanced searchFor detailed search
#6 Blast searchBy sequence similarity
#5 Sample viewsJump to each sample view
#7 H-InvDB NaviNavigation system
#4 Site mapJump to each sample view
H-InvDB Application#1-1H-InvDB Application#1-1
“Genes of certain feature”• Recommended entry points:
1. Search by simple search2. 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#1-2H-InvDB Application#1-2
“Genes of certain feature”• Recommended entry points:
1. Search by simple search
2. Search by advanced search3. 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#1-3H-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#2H-InvDB Application#2
“New sequence”“New sequence”
Blast search
H-InvDB annotation data formatH-InvDB annotation data format
• 3 annotation data formats
JBIRC flat file format DDBJ flat file format
JBIRC XML file format
H-InvDB data download sitesH-InvDB data download sites
• 2 data download sites1. HTTP site2. FTP site
Jump to Download
H-InvDB top page
HTTP download site
Downloading annotated data
H-InvDB data download pageH-InvDB data download page
• 2 data download site1. HTTP site
2. FTP site
Jump to FTP server
H-InvDB official page
Downloading annotated data
FTP download site
H-InvDB annotation data downloadH-InvDB annotation data download
• Data download from each view1. 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 downloadH-InvDB annotation data download
• Data download from each view1. JBIRC flat file format
2. JBIRC XML format
3. DDBJ format
4. Sequence FASTA files
Transcript view
Select at pull-down menuand click on “Download”
H-InvDB documentationH-InvDB documentation
1. About H-Invitational project
2. Help documents1. 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-InvDBContact 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 !!
AcknowledgementsAcknowledgements
• 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.