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4.13 Gene families/group view

The Gene family/Group view provides annotation datasets for human gene family/groups. We provide human-curated annotation datasets for the four selected gene families/groups, and predicted annotation datasets. 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.

Human-curated annotation datasets for selected gene families/groups
We provide human-curated annotation datasets for the four selected gene families/groups. 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. Each page provides the list of genes, gene names, definitions and links for the appropriate H-InvDB views.

Predicted gene families/groups (auto-annotated datasets)

icon_HIFWe predicted the gene family/groups for human gene dataset. 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 (InterPro).


Fig. 4.13.1. Gene family/group view


Access to H-InvDB Gene Families/Groups view

http://www.h-invitational.jp/hinv/genefamily/index_en.cgi

1) H-InvDB top page

You can access to H-InvDB Gene Families/Groups view via two entry points at H-InvDB top page.

To jump to the top page of the H-InvDB Gene Families/Groups, please click on Gene Families/Groups or gene families/groups in the sentence of "What is H-InvDB".


Fig. 4.13.2 The entry points at the H-InvDB top page


2) Locus view and Transcript view

You can jump to the top page of H-InvDB Gene Families/Groups view by clicking on "icon_GFAGene Family/Group"at the top of Locus view or Transcript view.

In addition, you can click on "icon_GFA" in Locus view and Transcript view to jump to the each corresponding gene family/group view.


Fig. 4.13.3 The entry points at Locus view


4.13.1 Ig: immunoglobulin (HIF0000001)

Immunoglobulin (Ig) is essential for the immune responses, and expressed at the surface of the B cells or secreted by the plasma cells. Ig is composed of the polypeptide chains with two different characters: heavy and light chains (κ,λ).
H-InvDB Ig annotation dataset was intended to include the genes of heavy and light chains (κ,λ). Ig-like genes and non-Ig genes (ex. VpreB, T-cell receptor) were excluded. The H-InvDB Ig dataset was defined by genomic location obtained from literature, sequence similarity search using a standard protein dataset, keyword search against sequence description and manual curation.

4.13.1.1 Access to the Ig view

http://www.h-invitational.jp/hinv/genefamily/geneFamilyIG_en.cgi
To display Ig view, please click on "Ig" or "Ig: immunoglobulin" in the top page of H-InvDB Gene Families/Groups.

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Fig. 4.13.1.1 The top page of H-InvDB Gene Families/Groups


4.13.1.2 Page layout of the Ig view

In the Ig view, we provide "the description of the H-InvDB Ig annotation dataset" and "Information about Ig H-Inv locus".

    We provide information about Ig H-Inv locus as below.
  1. HIX ID
    This column displays HIX ID of H-InvDB Ig annotation dataset.
    HIX ID links to Locus view.

  2. Chr. Location
    This column displays chromosome number of Ig H-Inv locus.
    Chromosome number links to G-integra.

  3. HGNC gene symbol
    This column displays HGNC gene symbol (HGNC).
    HGNC gene symbol links to the HUGO Gene Nomenclature Committee.

  4. Definition
    This column displays the definition of Ig H-Inv locus.

  5. IMGT/GENE-DB
    This column displays IMGT gene name related to Ig H-Inv locus.
    IMGT gene name links to IMGT/GENE-DB.
    IMGT/GENE-DB is genome database for Ig and TCR gene provided by IMGT® (the international ImMunoGeneTics information system®).
HUGO Gene Nomenclature Committee
URL http://www.genenames.org/index.html

IMGT
URL http://imgt.cines.fr/


Fig. 4.13.1.2 Page layout of the Ig view


4.13.1.3 Download

You can download H-InvDB Ig annotation dataset. Please click on [Download] in Ig view.

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Fig. 4.13.1.3 Download


4.13.2 MHC: major histocompatibility complex (HIF0000002)

GFA/MHC page (http://www.h-invitational.jp/hinv/genefamily/geneFamilyMHC_en.cgi) provides manually annotated datasets extracted by below methods from H-InvDB transcripts.

4.13.2.1 The methods for extracting of MHC candidate gene

Based on keyword
We set the keyword for searching MHC candidate gene to H-InvDB description and DDBJ flat file.
keyword:HLA, MHC, major histocompatibility complex and human leukocyte antigen

Based on sequence similarity
We run blastx for selecting the representative MHC protein from UniProt database and extract the sequence with identity more than 80%.
UniProt entry:P01903 (HLA-DRA), P01909 (HLA-DQA1), P01919 (HLA-DQB1), P04229 (HLA-DRB1), P20036 (HLA-DPA1), P30443 (HLA-A), P30460 (HLA-B), P30499 (HLA-C), Q30174 (HLA-DPB1)

Based on genome location http://www.sanger.ac.uk/HGP/Chr6/XMHC/xlist.shtml
We get the genome location for RefSeq gene in above xMHC map and extract the gene overlapped with RefSeq gene.
xMHC map reference:Gene map of the extended human MHC. Nat Rev Genet. 2004 Dec;5(12):889-99.

4.13.2.2 Access to GFA/MHC page

To display MHC view, please click on "Ig" or "MHC: major histocompatibility complex" in the top page of H-InvDB Gene Families/Groups.

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Fig. 4.13.2.1 The top page of H-InvDB Gene Families/Groups


4.13.2.3 Main parts of GFA/MHC page


Fig. 4.13.2.2 Summary of GFA/MHC page


  1. Link to Locus view of H-InvDB
  2. Link to G-integra
  3. Link to HGNC (HUGO Gene Nomenclature Committee)
  4. Tables are sorted by each haplotype.

4.13.3 TCR: T-cell receptor (HIF0000003)

T-cell receptors (TCRs) are antTCRen-specific receptors found on the cell surface of T-lymphocytes and are essential for the immune responses. TCRs are heterodimers consisting of alpha and beta, or gamma and delta chains that recognize specific antigens presented by MHC molecules on antigen-presenting cells.
The H-InvDB TCR dataset was defined by sequence homology search against standard TCR proteins, genomic location obtained from literature, keyword search against sequence description and manual curation

4.13.3.1 Access to the TCR view

http://www.h-invitational.jp/hinv/genefamily/geneFamilyTCR_en.cgi
To display TCR view, please click on "TCR" or "TCR: T-cell receptor" in the top page of H-InvDB Gene Families/Groups.

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Fig. 4.13.3.1 The top page of H-InvDB Gene Families/Groups


4.13.3.2 Page layout of the TCR view

In the TCR view, we provide "the description of the H-InvDB TCR annotation dataset" and "Information about TCR H-Inv locus".

    We provide information about TCR H-Inv locus as below.

  1. HIX ID
    This column displays HIX ID of H-InvDB TCR annotation dataset.
    HIX ID links to Locus view.

  2. Chr. Location
    This column displays chromosome number of TCR H-Inv locus.
    Chromosome number links to G-integra.

  3. HGNC gene symbol
    This column displays HGNC gene symbol (HGNC).
    HGNC gene symbol links to the HUGO Gene Nomenclature Committee.

  4. Definition
    This column displays the definition of TCR H-Inv locus.

  5. IMGT/GENE-DB
    This column displays IMGT gene name related to TCR H-Inv locus.
    IMGT gene name links to IMGT/GENE-DB.
    IMGT/GENE-DB is genome database for Ig and TCR gene provided by IMGT® (the international ImMunoGeneTics information system®).
HUGO Gene Nomenclature Committee
URL http://www.genenames.org/index.html

IMGT
URL http://imgt.cines.fr/


Fig. 4.13.3.2 Page layout of the TCR view


4.13.3.4 Download

You can download H-InvDB TCR annotation dataset. Please click on [Download] in TCR view.

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Fig. 4.13.3.3 Download


4.13.4 OR: olfactory receptor (HIF0000004)

4.13.4.1. Access to OR view

Please enter Olfactory Receptor (OR) page from either links of a blue button ORor a text 'OR: olfactory receptor' in the Gene family/group page (http://www.h-invitational.jp/hinv/genefamily/index_en.cgi), which are marked by red circles (Fig. 4.13.4.1).


Fig. 4.13.4.1 Gene family/group page


4.13.4.2. The contents of OR view

After moving OR genes page (http://www.h-invitational.jp/hinv/genefamily/geneFamilyOR_en.cgi), you could see a list of H-InvDB's OR genes. First row represents contents of each column (Fig. 4.13.4.2).

Fig. 4.13.4.2 OR genes page and OR gene


4.13.4.3. OR data download

The table can be downloaded from the link, '[Download ORs in H-InvDB]'(Fig. 4.13.4.3).


Fig. 4.13.4.3 data download


4.13.4.3. OR annotation policy

H-InvDB OR gene family includes the following genes; the genes predicted based on the method of modified Niimura and Nei (2003, PMID: 14507991), the OR genes registered in other databases (Invitrogen, cdna.org, origene, GPCR-DB, SEVENS), and the genes listed by the results of keyword search in sequence description.

From the download link named [Download ORs of Niimura & Nei(2003) (nucleotide_seq, amino_acid_seq)], you can obtained the nucleotide and amino acid sequences of the OR gene family predicted based on the method of modified Niimura and Nei (Fig. 4.13.4.3). Since these genes are predicted using the human genome only, there might be genes that have no corresponding transcripts in our H-InvDB, or some differences in the sequence or length from its corresponding transcripts. Also the genes obtained from other DB or the results of keyword search are not included in the file.

Revised: February 29, 2008.