• IMGT/GeneFrequency is part of IMGT, the international ImMunoGeneTics information system®, http://www.imgt.org [1].
  
  IMGT/GeneFrequency, created by LIGM (Université Montpellier II, CNRS), on the Web since August 2003, is a tool which provides a graphical representation of the numbers of cDNA and genomic IMGT/LIGMDB sequences containing rearranged immunoglobulin (IG) and T cell receptor (TR) genes.
  
  
• Gene frequency is calculated for fully annotated IG and TR rearranged sequences (cDNA and genomic DNA) extracted from IMGT/LIGM-DB, according to the user query. IMGT/GeneFrequency results are shown as graphical representations which comprise histograms localized at the V, D and J gene positions along the locus and proportional to the number of IMGT/LIGM-DB cDNA and genomic sequences containing that gene and answering the user selection (IMGT Repertoire>Locus representations).
  Clicking on the bars of the histogram gives access to IMGT/GENE-DB and IMGT/LIGM-DB entries answering the user selection.
  
  
• Sequences extracted by IMGT/GeneFrequency from IMGT/LIGM-DB are necessarily fully annotated, either manually (indicated by "annotators" in the ID line of the flat files, example: AF306358) or by the IMGT/Automat tool [2] ("automatic" in the ID line, example: AF306350). These flat files contain the IMGT gene names [3,4] which are required for the search by the IMGT/GeneFrequency tool. Note that genomic DNA sequences which contain more than one V gene [for instance, one rearranged V-D-J gene and one (or several) germline gene(s)] are not available to the query.
  
  

In the IMGT/GeneFrequency Search page, the selection takes place in three stages:

1. Select a Species:
   
   

   At present only Homo sapiens and Mus musculus sequences are available.

   
   
   
   
2. Histogram for:
   
   
   • All IMGT/LIGM-DB rearranged sequences
   • or Specificity (choice in a multiple list, for example "anti-thyroid peroxidase (TPO)")
   
   Following the specificity choice, only the loci that contain genes which answer the selected specificity will be offered for selection in the "Individual locus" box.
   
   
   
   
3. Select Loci:
   
   
   1. IG or TR loci:
      
      
      • IGH, IGK, IGL, for immunoglobulin
        
      • TRA/TRD, TRB, TRG, for T cell receptor
        
      
      The scale depends on the locus length.
      
      
   2. Individual locus:
      
      
      • IGH
      • IGK
      • IGL
      • TRA/TRD
      • TRB
      • TRG
      
      
   Two different scales (200 kb per line or 400 kb per line) are available, select a scale to visualize the locus.
   
   
   
   
4. Click on the "Search" button to valid your search.

Results for All IMGT/LIGM-DB rearranged sequences (IG or TR loci)

The IMGT/GeneFrequency results for all IMGT/LIGM-DB rearranged sequences (IG or TR loci) query comprise:

• Title
  
  The title indicates the species, the IG loci (IGH, IGK, IGL) or the TR loci (TRA/TRD, TRB, TRG)
  
  
• Graphical representation
  
  
  • The three IG loci (IGH, IGK and IGL) or the four TR loci (TRA/TRD, TRB and TRG) are displayed, depending on the selection.
    The scale depends on the locus length.
    
    
  • The graphical representation comprises histograms localized at the V-GENE, D-GENE and J-GENE positions in the locus.
    
    
    • Gene positions are from IMGT/LocusView. Only genes that have rearranged sequences answering the query (species, specificity, loci) are displayed.
      
    • The height of the vertical bar is proportional to the number of IMGT/LIGM-DB cDNA and genomic sequences containing a given gene and answering the user selection. The color of the vertical bar indicates the gene type, according to IMGTScientific Chart>Color Menu.
      
    
    
  • The C genes are shown by squares.
  
  
• Zoom

  
  A zoom is available for D-GENEs and J-GENEs by clicking on the corresponding areas.

  
  
• Results summary (Number of sequences per locus and per gene)

  
  A summary table gives access to the number of IMGT/LIGM-DB sequences with rearranged gene foreach locus, Group and Gene. Clicking on numbers gives access to the detailled list of IMGT/LIGM-DB sequences (accession number and description).
  Clicking on loci or groups gives access to the corresponding section in the table.

Results for All IMGT/LIGM-DB rearranged sequences (Individual locus)

The selected locus (IGH, IGK, IGL, TRA/TRD, TRB or TRG ) is displayed depending on the selection, and in the chosen scale (200 kb or 400 kb).
The IMGT/GeneFrequency results for "Individual locus" query comprise:

• Title

  
  The title indicates the species and the locus with its chromosomal localization IMGTRepertoire>Chromosomal localizations.

  
  
• Graphical representation
  
  
  • The graphical representation comprises histograms localized at the V-GENE, D-GENE and J-GENE positions in the locus.
    • Gene positions are from IMGT/LocusView. Only genes that have rearranged sequences answering the query (species, specificity, locus) are displayed.
      
    • The height of the vertical bar is proportional to the number of sequences answering the query in IMGT/LIGM-DB. The color of the vertical bar indicates the gene type, according to IMGTScientific Chart>Color Menu.
    
    
  • The C genes are shown by squares.
  
  
• Zoom

  
  A zoom is available for D-GENEs and J-GENEs by clicking on the corresponding areas.

Results for Specificity (IG or TR loci)

The IMGT/GeneFrequency results for selected specificity (IG or TR loci) query comprise:

• Title
  
  The title indicates the species, the IG loci (IGH, IGK, IGL) or the TR loci (TRA/TRD, TRB, TRG)
  
  
• Graphical representation
  
  
  • The three IG loci (IGH, IGK and IGL) or the four TR loci (TRA/TRD, TRB and TRG) are displayed, depending on the selection.
    The scale depends on the locus length.
    
    
  • The graphical representation comprises histograms localized at the V-GENE, D-GENE and J-GENE positions in the locus.
    
    
    • Gene positions are from IMGT/LocusView. Only genes that have rearranged sequences answering the query (species, specificity, loci) are displayed.
      
    • The height of the vertical bar is proportional to the number of IMGT/LIGM-DB cDNA and genomic sequences containing a given gene and answering the user selection. The color of the vertical bar indicates the gene type, according to IMGTScientific Chart>Color Menu.
      
    
    
  • The C genes are shown by squares.
  
  
  
• Zoom


• A zoom is available for D-GENEs and J-GENEs by clicking on the corresponding areas.



• Information for all genes


• For each locus and for each gene, the IMGT/LIGM-DB cDNA and genomic sequences with rearranged genes are indicated.

Results for specificity (Individual locus)

The selected locus (IGH, IGK, IGL, TRA/TRD, TRB or TRG ) is displayed depending on the selection, the chosen specificity and in the chosen scale (200 kb or 400 kb).
The IMGT/GeneFrequency results for "Individual locus" query comprise:

• Title

  
  The title indicates the species, the specificity (selected in the IMGT/GeneFrequency Search page), and the locus with its chromosomal localization

  
  
• Graphical representation
  
  
  • The graphical representation comprises histograms localized at the V-GENE, D-GENE and J-GENE positions in the locus.
    • Gene positions are from IMGT/LocusView. Only genes that have rearranged sequences answering the query (species, specificity, locus) are displayed.
      
    • The height of the vertical bar is proportional to the number of sequences answering the query in IMGT/LIGM-DB. The color of the vertical bar indicates the gene type, according to IMGTScientific Chart>Color Menu.
    
    
  • The C genes are shown by squares.
  
  
  
• Zoom


• A zoom is available for D-GENEs and J-GENEs by clicking on the corresponding areas.



• Information for all genes


• For each locus and for each gene, the IMGT/LIGM-DB cDNA and genomic sequences with rearranged genes are indicated.

Access to IMGT/LIGM-DB and IMGT/GENE-DB:

Clicking on the vertical bar of a gene gives access to a link to IMGT/GENE-DB entry for that gene an to a list of IMGT/LIGM-DB accession numbers answering to the user selection.
Each IMGT/LIGM-DB accession number has a link to the resulting page in IMGT/LIGM-DB and the IMGT/GENE-DB entry for the gene has a link to the resulting page in IMGT/GENE-DB.

Particularities of the IGK locus:

• Eight genes of the IGK distal cluster (IGKV1D-12, IGKV1D-13, IGKV1D-33, IGKV1D-37, IGKV1D-39, IGKV2D-28, IGKV2D-40 and IGKV6D-21) have a high similarity with the corresponding genes from the proximal cluster (IGKV1-12, IGKV1-13, IGKV1-33, IGKV1-37, IGKV1-39, IGKV2-28, IGKV2-40 and IGKV6-21, respectively). Expressed sequences cannot be therefore assigned to the proximal or distal gene. For these 8 gene pairs, in IMGT/GeneFrequency, the expressed sequences are assigned to the gene of the proximal cluster. Indeed, there is only a very low probability that expressed sequences are from genes of the distal cluster for the following reasons: distance from the J genes superior to 1300 kb, mechanism of inversion for the V-J rearrangements.
• For the other genes of the distal cluster, IMGT/GeneFrequency allows a normal histogram representation, if by any chance, expressed sequences are found.

See also:

• Annotations
  
• Classification
  
• Gene
  
• Gene type
  
• IMGT Repertoire
  
• IMGT Scientific Chart
  
• Locus
  
• Molecule type
  
• Nomenclature
  
• Species
  
• Specificity
  

References:

[1] Lefranc, M.-P., Nucleic Acids Res., 33, D593-D597 (2005), PMID:15608269, LIGM:291.
[2] Giudicelli V., Protat C., and Lefranc M.-P., The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/Automat, European Conference on Computational Biology ECCB 2003
[3] Lefranc, M.-P. and Lefranc, G., The Immunoglobulin FactsBook, Academic Press, 458 pages (2001) ISBN:012441351X
[4] Lefranc, M.-P. and Lefranc, G., The T cell receptor FactsBook, Academic Press, 398 pages (2001) ISBN:0124413528

The IMGT/GeneFrequency tool was implemented using Perl (CGI, GD, SOAP, DBI, DBD) (DESS Bioinformatique, Université Montpellier II, France, stage at LIGM, Montpellier 14/04/03-31/08/03).

IMGT/GeneFrequency Documentation was written by Stéphanie Jeanjean, Elodie Boucomont (1ère année DUT Génie Biologique option Bioinformatique, IUT Clermont-Ferrand, antenne Aurillac, stage at LIGM, Montpellier 01/07/03-15/08/03) and François Ehrenmann Francois.Ehrenmann@igh.cnrs.fr.

The IMGT/GeneFrequency tool has been improved by François Ehrenmann and Marie-Paule Lefranc for an easier access on the web in July 2006.

Contact IMGT/GeneFrequency Montpellier, France :
François Ehrenmann Francois.Ehrenmann\@igh.cnrs.fr and Marie-Paule Lefranc Marie-Paule.Lefranc\@igh.cnrs.fr

Authors: François Ehrenmann, Stéphanie Jeanjean and Marie-Paule Lefranc

Created: 30/06/2003
Last updated: 31/07/2006

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-> IMGT/GeneFrequency Search page
-> IMGT/GeneFrequency Documentation

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Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT, and cited as \"IMGT, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France).\" References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001); Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003); Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text.
For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc\@igh.cnrs.fr.

     

IMGT founder and director: Marie-Paule Lefranc Marie-Paule.Lefranc\@igh.cnrs.fr
Bioinformatics manager: Véronique Giudicelli Veronique.Giudicelli\@igh.cnrs.fr
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