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1.0 What is H-InvDB?

1.0.1 H-Invitational database

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, 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 consists of three main views, Transcript view, Locus view and Protein view, and six sub-databases with web-based viewers; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view, and provided as flat files, XML files and sequence fasta files.

1.0.2 H-InvDB identifiers

Annotations in H-InvDB are assigned to individual transcript or cluster or protein. We also defined and assigned the unique identifiers for proteins and gene family/group. We defined a unique identifier for each of those annotation units as follows

HIT (H-Invitational transcript):

Prefix HIT plus 9 digit numbers plus version_number; e.g. HIT000000001.1

We defined an HIT ID for each H-Inv cDNA, mRNA or RNA entry, which is a stable and unique identifier for each H-Invitational transcript. In order to identify the modification in sequence or annotation of an H-Inv transcript entry, an HIT version is assigned to each HIT ID and always stated with the HIT ID.

*1) For eHIT gene models (refer to 2.0.3 for the details), we assigned HIT ID with additional geh at the prefix;
Prefix eHIT plus 9 digit numbers plus version_number; e.g. eHIX000000001.1

*2) For pHIT gene models (refer to 2.0.4 for the details), we assigned HIT ID with additional gph at the prefix;
Prefix pHIT plus 9 digit numbers plus version_number; e.g. pHIX000000001.1

*3) Transcript which locate multiple locations on the genome are assigned HIT ID with additional multi-location_number plus version_number; eg HIT000000001_01.1 for each transcript

HIX (H-Invitational cluster):

Prefix HIX plus 7 digit numbers plus version_number; e.g. HIX0000001.1

We defined an HIX ID for each H-Inv cluster, which is a stable and unique identifier for each H-Inv cluster. A unique HIX ID is assigned to each H-Inv transcript entry identifying the location in the human genome or the unmapped cluster. In order to identify the modification in location in the human genome or annotation of the H-Inv cluster entry, an HIX version is assigned to each HIX ID and always stated with the HIX ID.

HIP (H-Invitational protein):

Prefix HIP plus 9 digit numbers plus version_number; e.g. HIP000000001.1

We defined an HIP ID for each unique translation, which is a stable and unique identifier for each H-Invitational protein.

HIF (H-Invitational gene family/group):

Prefix HIF plus 7 digit numbers; e.g. HIF0000001

We defined an HIF ID for each H-Inv gene family/group, which is a stable and unique identifier for each H-Inv gene family/group. A unique HIF ID is assigned to each group of H-Inv cluster entries identifying the groupings of the human gene in a context of sequence similarity and conservation of functional motif.

1.0.3 Views and databases in H-InvDB

H-InvDB consists of three main views, Transcript view, Locus view and Protein view, and six sub-databases with web-based viewers; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view, and provided as flat files, XML files and sequence fasta files.


Fig 1.0.3 Views and databases in H-InvDB

Transcript view

H-InvDB provides annotation items for each HIT (H-Invitational transcript) in Transcript view, such as gene function, predicted CDS, GO, 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.

Protein view

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

G-integra

G-integra is a genome integrated database, in which we can browse physical maps of human and related animal genome and the gene structures.

H-ANGEL

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.

Evola

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

The PPI view displays H-InvDB human protein-protein interaction (PPI) information.

Gene Family/Group

H-InvDB Gene Families/Groups are human-curated annotation datasets for the selected gene families/groups.

1.0.4 Guidance for H-InvDB

Possible applications of H-Invitational Database to Biomedical Researches are described in "H-InvDB_tutorial.ppt", where we demonstrate about following topics;

    >>>H-InvDB entry points to annotated data
    >>>H-InvDB application#1
         *"If you look for gene of certain feature"
    >>>H-InvDB application#2
         *"If you have special interests in certain location in human genome"
    >>>H-InvDB application#3
         *"If you sequenced a new gene"
    >>>H-InvDB annotation data download
    >>>Documentation
    >>>Contact to H-InvDB
Revised: February 16, 2010