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IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST

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ABSTRACT

There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the “IMGT clonotype (AA)” (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for “IMGT clonotype (AA)” diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT® tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package “IMGTStatClonotype,” with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT®1 for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V–D–J associations, in immunoprofiles from normal or pathological immune responses.

No MeSH data available.


IMGT/StatClonotype V–D–J gene associations. “V–D–J gene associations” displays heatmaps to represent V–J, V–D, or D–J gene associations in sets 1 and 2. Heatmaps are downloadable in different formats (PNG, JPG, and PDF). Under heatmaps, tables crossing the V–J, V–D, or D–J gene occurrences in sets 1 and 2 are given and downloadable in csv files. The clustered heatmaps of the V–J associations in sets 1 and 2 are shown as examples.
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Figure 7: IMGT/StatClonotype V–D–J gene associations. “V–D–J gene associations” displays heatmaps to represent V–J, V–D, or D–J gene associations in sets 1 and 2. Heatmaps are downloadable in different formats (PNG, JPG, and PDF). Under heatmaps, tables crossing the V–J, V–D, or D–J gene occurrences in sets 1 and 2 are given and downloadable in csv files. The clustered heatmaps of the V–J associations in sets 1 and 2 are shown as examples.

Mentions: In the right panel (Figure 1), users can choose among eight tabs at the top: “IMGT/HighV-QUEST set 1,” “IMGT/HighV-QUEST set 2,” “Statistical test results,” “Multiple testing procedures plots,” “Synthesis graphs,” “CDR-IMGT lengths,” “CDR-IMGT AA properties,” and “V-D-J gene associations.” The display shown is for “IMGT/HighV-QUEST set 1.” A similar display is obtained for “IMGT/HighV-QUEST set 2.” The six other tabs correspond to table and graph results displays, described in the section “Results” (Figures 2–7). For each display, users can select corresponding parameters in the left panel.


IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST
IMGT/StatClonotype V–D–J gene associations. “V–D–J gene associations” displays heatmaps to represent V–J, V–D, or D–J gene associations in sets 1 and 2. Heatmaps are downloadable in different formats (PNG, JPG, and PDF). Under heatmaps, tables crossing the V–J, V–D, or D–J gene occurrences in sets 1 and 2 are given and downloadable in csv files. The clustered heatmaps of the V–J associations in sets 1 and 2 are shown as examples.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5016520&req=5

Figure 7: IMGT/StatClonotype V–D–J gene associations. “V–D–J gene associations” displays heatmaps to represent V–J, V–D, or D–J gene associations in sets 1 and 2. Heatmaps are downloadable in different formats (PNG, JPG, and PDF). Under heatmaps, tables crossing the V–J, V–D, or D–J gene occurrences in sets 1 and 2 are given and downloadable in csv files. The clustered heatmaps of the V–J associations in sets 1 and 2 are shown as examples.
Mentions: In the right panel (Figure 1), users can choose among eight tabs at the top: “IMGT/HighV-QUEST set 1,” “IMGT/HighV-QUEST set 2,” “Statistical test results,” “Multiple testing procedures plots,” “Synthesis graphs,” “CDR-IMGT lengths,” “CDR-IMGT AA properties,” and “V-D-J gene associations.” The display shown is for “IMGT/HighV-QUEST set 1.” A similar display is obtained for “IMGT/HighV-QUEST set 2.” The six other tabs correspond to table and graph results displays, described in the section “Results” (Figures 2–7). For each display, users can select corresponding parameters in the left panel.

View Article: PubMed Central - PubMed

ABSTRACT

There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the “IMGT clonotype (AA)” (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for “IMGT clonotype (AA)” diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT® tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package “IMGTStatClonotype,” with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT®1 for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V–D–J associations, in immunoprofiles from normal or pathological immune responses.

No MeSH data available.