Download Help - H-Invitational database!!

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
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

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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.