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.