GeneFrequency logo

IMGT/GeneFrequency documentation

Program version :
2.0.0 (24/08/2016)
Citing:
Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005). PMID:15972004, LIGM:294 In Silico Biol., 5, 0006 (2004) Abstract

Introduction

IMGT/GeneFrequency is part of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org [1]

IMGT/GeneFrequency, created by LIGM (Université de Montpellier, CNRS) and on the Web since 2003 [2], was completely re-written and upgraded in 2016 [3].

IMGT/GeneFrequency is an IMGT® tool that provides a graphical and tabular representation, per immunoglobulin (IG) [4] or T cell receptor (TR) [5] locus, of the numbers of IMGT/LIGM-DB cDNA rearranged sequences assigned to the variable (V), diversity (D, joining (J) and constant (C) genes [6].

The sequences taken into account are fully annotated IG and TR rearranged sequences from IMGT/LIGM-DB [7], either manually or by the IMGT/Automat tool [8, 9] (see the “IMGT annotation level” field of the IMGT/LIGM-DB entries) and available, per gene, in IMGT/GENE-DB [10], e.g., ‘Table of annotated IMGT/LIGM-DB cDNA rearranged sequences’.

Good to know

IGMT/GeneFrequency query page

IMGT/GeneFrequency query page

The IMGT/GeneFrequency query page allows the selection of the desired species, specificity and IG or TR locus to show on the graph. Selecting “any” in the specificity field will query all sequences regardless of their specificity.

When selecting a species, the specificity and locus dropdowns will be refreshed to show only appropriate choices for that species.
Similarly, when a specificity is selected, the locus dropdown will be refreshed and restricted to appropriate choices for that specificity.
Hence, the selection should always be made in the Species -> Specificity -> Locus order.

IMGT/GeneFrequency graph of cDNA rearranged sequences

Header

Header of the IMGT/GeneFrequency graph of cDNA rearranged sequences

On the top of the page, there is a form which permits to quickly change the selection. It works similarly to the form at the IMGT/GeneFrequency query page.
The section “Displaying” recalls the current selection.

The section “Sequence counts” gives the total number of unique sequences found for each gene group. One individual sequence (=one accession number) will be counted for each relevant group. However, a sequence will never be counted more than once for a given group.

Clicking on “Switch to list view” displays the graph results in tabular form (see the IMGT/GeneFrequency list of rearranged sequences section).

IMGT/GeneFrequency graph

Main graph

IMGT/GeneFrequency graph of cDNA rearranged sequences

The graph is a bar chart that presents the number of IMGT/LIGM-DB cDNA rearranged sequences for each V, D or J gene of the selected IG or TR locus. The genes are placed at fixed intervals and ordered according to the Gene Order concept (defined in LOCALIZATION (IMGT Index). All genes are shown, even those which do not have any cDNA rearranged. sequences.

A bar of the graph is potentially divided in two parts:

The name of a gene is followed by the functionalities of its alleles (i.e, F, [F], (F)) as described in Functionality IMGT Index.

Hovering the mouse on a bar displays the number of cDNA rearranged sequences for that gene.

Clicking on the bar or the name of a gene which has at least one cDNA rearranged sequence, opens the IMGT/GENE-DB ‘Table of annotated IMGT/LIGM-DB cDNA rearranged sequences’ (Accession number, Allele name, Sequence length, Sequence definitions, Specificity(ies) ) for that gene. From there, individual IMGT/LIGM-DB entries for each sequence can be accessed.

C-GENES are represented with a simple square instead of a bar. However, clicking on the box will open the IMGT/GENE-DB table of ‘annotated IMGT/LIGM-DB cDNA rearranged sequences’ for that gene, as above.

Zoom graph

IMGT/GeneFrequency graph of cDNA rearranged sequences : D/J zoom

If the locus is more than 20 genes long, D-GENE and J-GENE will be extracted into separate graph(s) named D/J zooms. Note that zoom graphs may have a different vertical scale than the main graph.

IMGT/GeneFrequency graph of cDNA rearranged sequences : Zoom indicator highlight

The position of these zooms on the main graph are represented by a red zoom indicator. Clicking on a zoom indicator will jump to the corresponding zoom graph.

Not localized genes

Genes which belong to the locus, but which are not localized (gene order ‘0’), are placed in a separate graph below the zooms titled “Not localized genes”. These genes are sorted by alphabetical order.

Downloading the graph

To download a .png image of the graph currently being displayed, use the “Download this graph as a .png image” link at the bottom of the page. Generation of the file may take a few seconds.

IMGT/GeneFrequency list of cDNA rearranged sequences

Header

The header is the same as the one on the graph page.

IMGT/GeneFrequency list

IMGT/GeneFrequency list of cDNA rearranged sequences

Each gene group is listed in a table, where the genes are sorted by name. In contrast to the graph, only the genes which have cDNA rearranged sequences associated with them are shown.

The tables have four columns:

At the bottom of each table, the sum of each column is calculated for practical purposes. However it should be remembered that the number of sequences of the white part is counted at least twice (as present on at least two bars on the graph). In contrast, the unique sequence counts are shown at the top of the page.

Clicking on a gene name will open the IMGT/GENE-DB ‘Table of annotated IMGT/LIGM-DB cDNA rearranged sequences’ (Accession number, Allele name, Sequence length, Sequence definitions, Specificity(ies) ) for that gene. From there, individual IMGT/LIGM-DB entries for each sequence can be accessed.

References

[1] Lefranc, M.-P. et al. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res., 43, D413-22 (2015), PMID: 25378316, LIGM:441

[2] Lefranc et al. IMGT-Choreography for immunogenetics and immunoinformatics. In Silico Biol. 2005; 5(1)45-60. PMID: 15972004, LIGM:294

[3] Klein V, Giudicelli V, Kossida S., Lefranc M-P and Duroux P. IMGT/GeneFrequency Upgrade 2016 (11/08/2016)

[4] Lefranc, M.-P. and Lefranc, G., The Immunoglobulin FactsBook, Academic Press, 458 pages (2001) ISBN:012441351X

[5] Lefranc, M.-P. and Lefranc, G., The T cell receptor FactsBook, Academic Press, 398 pages (2001) ISBN:0124413528

[6] Lefranc M-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. 2014 Feb 05;5:22. Open access. PMID: 24600447, LIGM:429

[7] Giudicelli, V., Duroux, P., Ginestoux, C., Folch, G., Jabado-Michaloud, J., Chaume, D. and Lefranc, M.-P. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res., 34, D781-D784 (2006). PMID: 16381979, LIGM:307

[8] 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, Proceedings of the European Conference on Computational Biology (ECCB 2003), INRIA (DISC/Spid), Paris, DKB-31, pp.103-104

[9] Giudicelli, V., Chaume, D., Jabado-Michaloud, J. and Lefranc, M.-P. Immunogenetics sequence annotation: the strategy of IMGT based on IMGT-ONTOLOGY. Stud. Health Technol. Inform. 2005, 116, 3-8. PMID: 16160227, LIGM:298

[10] Giudicelli, V., Chaume, D. and Lefranc, M.-P. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res., 33, D256-D261 (2005). PMID: 15608191, LIGM:292

IMGT/GeneFrequency implementations and developments

August 2003 -> August 2016 IMGT/GeneFrequency program version 1

The IMGT/GeneFrequency tool was implemented using Perl (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 (01/07/03-15/08/03) and François Ehrenmann.
The IMGT/GeneFrequency tool has been improved by François Ehrenmann and Marie-Paule Lefranc for an easier access on the web in July 2006 (31/07/06).
The IMGT/GeneFrequency tool has been maintained and improved by Patrick Duroux since 2012.

Since August 2016 IMGT/GeneFrequency program version 2

The current version 2 is a complete re-write in Java, by Valentin Klein (30/05/2016-26/08/16), of the original tool to achieve better interoperability and extensibility. It has been implemented and developed by Valentin Klein, Véronique Giudicelli, Sofia Kossida, Marie-Paule Lefranc and Patrice Duroux.
It is maintained by Patrice Duroux.

Program versions

Version 2.0.0 (24/08/2016)

First public release of the new implementation of IMGT/GeneFrequency in Java. Design has received an overhaul. Important changes have been implemented. They are described in the IMGT/GeneFrequency Documentation « version 2.0 » upgrade page.

Version 1.2.1 (11/12/2015)

Version 1.2.0 (21/03/2014)

Version 1.1.0 (10/01/2011)

Improvement of IMGT/GeneFrequency Search page.
AJAX (Asynchronous JavaScript and XML) is used to create interactive web application. This AJAX technique makes IMGT/GeneFrequency smaller, faster and more user-friendly. With Ajax, the application can retrieve data from the server asynchronously in the background without interfering with the display and behavior of the existing page.

Version 1.0.1 (30/11/2010)

Improvement of IMGT/GeneFrequency Search page.

Created :
August 2016
Authors (current version) :
Valentin Klein, Patrice Duroux
Authors (original version) :
Stéphanie Jeanjean, François Ehrenmann, Patrice Duroux