H-InvDB Official Web Site [Japanese]

METI Life science integrated database portal site

MEDALS(METI Database portal for LifeScience) MEDALS
METI Database portal for Life Science
Hyperlink Management System Hyperlink Management System
MEDALS is a portal site that provides various information on databases and analysis tools for life science, which were developed by the projects directly sponsored by METI or the Institutes sponsored by METI. Hyperlink Management System is a tool for automatically updating and maintaining hyperlinks among major biological databases. We update correspondence tables of data IDs daily.

H-InvDB main views

Locus view Locus view
Locus annotation view
Transcript view Transcript view
Transcript annotation 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. 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).
Protein view Protein view
Protein annotation view

H-InvDB newly provides annotation items for each HIP (H-Invitational protein) in Protein view, such as protein function, subcellular localization, post-translational modification (PTM), protein 3D structure (GTOP), protein-protein interaction (PPI), etc.

H-InvDB sub-databases

G-integra G-integra
genome browser
Human ANatomic Gene Expression Library
G-integra is an original genome browser, in which we can browse physical maps of human, mouse, rat, chimpanzee, etc. genome and the gene structures. H-ANGEL is a database 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 each tissue.
Evola Evola
Evolutionary annotation database
DiseaseInfo Viewer DiseaseInfo Viewer
disease information database
Evola contains ortholog information among human and other vertebrates based on our analyses of comparative genomics and transcriptomics. Evola displays sequence alignments, phylogenetic trees and gene loci of orthologs. Comparison of orthologous gene families between species is also available. DiseaseInfo Viewer is a database of known and orphan genetic diseases and their relation to H-Inv loci with OMIM and MutationView.
PPI view PPI view
human protein-protein interaction (PPI)
Gene family/group Gene family/group
annotation of gene families/groups
The PPI view displays H-InvDB human protein-protein interaction (PPI) information. H-InvDB Gene Families/Groups are human-curated annotation datasets for the selected gene families/groups.

H-InvDB satellite databases&tools

Literature-Extracted GENe-Disease Associations
Transcriptome Auto-annotation Conducting Tool
LEGENDA stands for Literature-Extracted GENe-Disease Associations. It is a database based on the extraction of relations between genes, diseases, and substances from the entire MEDLINE titles and abstracts. 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.
database of the alternative splicing (AS)
VaryGene VarySysDB
database of annotated human polymorphism
H-DBAS is a database of human alternative splicing variants. The representative AS variants (RASV) were selected among AS variants which have the same genomic (exon-intron) structure. It offers annotated human polymorphism information of single nucleotide polymorphisms (SNPs) on splice sites and transcripts, deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), linkage disequilibrium regions, and their relations to the genome, transcripts, and functional domains.
DNAProbeLocator DNAProbeLocator
Web tool to map and browse DNA array probes
H-Exp H-Exp
Human gene expression profile database
DNAProbeLocator is a web-based display for the mapping of DNA array probes onto the human full-length cDNAs. H-Exp is a database of expression profiles of human genes. User can compare the expression profile of some gene with those of the other genes. Data can easily be sorted into expression profiles.
G-compass G-compass
Comparative genome browser
Web Service H-InvDB web service
G-compass visualizes conserved genomic regions between human and other vertebrates based on originally constructed genome alignments. Keyword search and BLAT search are implemented to access the regions. Substitution rate and other features of each genome alignment are graphically displayed. H-InvDB Web service provide the various SOAP and REST APIs to use H-InvDB data.
Any one can use the servise to develop the application using H-InvDB Web service.
Gene Diversity DataBase System(GDBS)
H-InvDB Enrichment Analysis Tool (HEAT)
A database of ca. 30,000 microsatellite markers, that were detected in silico from genome sequence and have been confirmed polymorphic in the Japanese population by the Genome Diversity Team. A data-mining tool for automatically identifying features specific to a given human gene set by searching H-InvDB.