Research
Integrated Database and Systems Biology Team develops an integrated database of all human genes and transcripts, H-Invitational Database (H-InvDB), and study biological phenomena such as evolution and gene expression by computational analyses of information about molecular systems. Also, we carry out the Integrated Database Project of Ministry of Economy, Trade, and Industry of Japan (METI) in collaboration with the Japan Biological Informatics Consortium (JBIC), in order to promote the use of databases in the field of life science.
About H-InvDB
H-InvDB http://www.h-invitational.jp/-
H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the "Genome Information Integration Project" (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs
H-InvDB provides annotation items for each transcript in Transcript view and gene locus in Locus view.
Transcript view
H-InvDB provides annotation items for each HIT (H-Invitational transcript) in Transcript view, such as gene function, predicted CDS, InterProScan, GO, subcellular localization, protein 3D structure (GTOP), evolutionary analysis, etc.
The previous name for the view was cDNA view (mRNA view).
Locus view
H-InvDB provides annotation items for each HIX (H-Invitational cluster) in Locus view, such as genome mapping, gene structure, alternative splicing variants, gene-expression profiles, disease related information, etc.
Sub databases
G-Integra http://www.h-invitational.jp/hinv/g-integra/html/- G-integra is a genome integrated database, in which we can browse physical maps of human, mouse, rat and chimpanzee genome and the gene structures.
H-Angel http://www.h-invitational.jp/hinv/h-angel/wge_top.cgi?- H-ANGEL (Human ANatomic Gene Expression Library) is a database of expression patterns that we constructed to obtain a broad outline of expression profiles of human genes. Gene expression data in normal adult human tissues that were generated by three types of methods and in seven different platforms were collected and categorized into 10 and 40 major tissues
DiseaseInfo Viewer - DiseaseInfo Viewer is a database of known and orphan genetic diseases and their relation to H-Inv loci with LocusLink, OMIM and GenAtlas.
TOPO - TOPO Viewer is a tool for viewing both subcellular targeting signals predicted by WoLF PSORT and TargetP, as well as the presence trans-membrane helices predicted by SOSUI and TMHMM
Clustering Viewer- Clustering Viewer is a viewer for comparisons of different clustering methods, mapping-based and cDNA-based clustering results.
Evola http://www.h-invitational.jp/evola/search.html- Evola is a database of evolutionary annotation of human genes. It provides sequence alignments and phylogenetic trees of ortholog genes among human and model organisms.
PPI view http://www.h-invitational.jp/hinv/ppi/- The PPI view displays H-InvDB human protein-protein interaction (PPI) information.
Satellite databases and tools
PANDA： Priority ANalysis for Disease Association- We constructed a ranking system to identify new disease genes, based on functional similarity to known disease genes.
LEGENDA：Literature-Extracted GENe-Disease Associations http://www.h-invitational.jp/legenda/- LEGENDA is a database of relations between diseases, genes, and substances extracted from a whole set of MEDLINE literatures.
H-GOLD: Human-Gene diversity Of Life-style related Disease http://jbirc.jbic.or.jp/gdbs/- A database of ca. 30,000 Microsatellite markers, which are detected in silico from genome sequence and confirmed polymorphism in Japanese population by Genome Diversity Team.
Evolgen: Evolutionary database of duplicate gene families- Evolgen is an evolutionary database of duplicate gene families. It provides orthologous relationship of the families and their member genes between human and other species.
G-compass：比較ゲノムウェブツール http://www.h-invitational.jp/g-compass/- G-compass is a web tool for comparative genomics, which can browse conserved regions based on the genome alignments of human-chimpanzee, human-mouse and human-rat. This provides BLAST search against the conserved regions and Keyword search by Gene symbol etc. Sliding window analysis of substitution rates and GC contents for each conserved region can be graphically shown in the Main view.
TACT：Transcriptome Auto-annotation Conducting Tool http://www.h-invitational.jp/tact/- TACT is a web-based automated prediction tool of functional annotation that was newly developed by integrating ORF prediction, similarity search (BLASTX and FASTY) and motif prediction (InterProScan) programs.
H-DBAS：Human DataBase of Alternative Splicing http://www.h-invitational.jp/h-dbas/- H-DBAS is a specialized database of the alternative splicing (AS) based on H-InvDB.
H-Inv DB Lineup
