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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

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.


IMGT/StatClonotype interface with its two panels. In the left panel, users choose the files of the two sets to be compared and can select the CDR3-IMGT length range of IMGT clonotypes (AA) (by default CDR3-IMGT lengths ≥4 AA and ≤45). In the right panel, 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 here is for “IMGT/HighV-QUEST set 1.”
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Figure 1: IMGT/StatClonotype interface with its two panels. In the left panel, users choose the files of the two sets to be compared and can select the CDR3-IMGT length range of IMGT clonotypes (AA) (by default CDR3-IMGT lengths ≥4 AA and ≤45). In the right panel, 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 here is for “IMGT/HighV-QUEST set 1.”

Mentions: The IMGT/StatClonotype interface comprises two panels. In the left panel (Figure 1), users choose the files of the two IMGT/HighV-QUEST sets to be compared. These files correspond, for each set, to the file “stats_xxx” from the data directory of the IMGT/HighV-QUEST statistical output and have to be previously uploaded by the user. Users can select the CDR3-IMGT length range of IMGT clonotypes (AA) to be analyzed (by default CDR3-IMGT lengths ≥4 AA and ≤45). CDR3-IMGT length outliers are eliminated from the statistical procedure.


IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST
IMGT/StatClonotype interface with its two panels. In the left panel, users choose the files of the two sets to be compared and can select the CDR3-IMGT length range of IMGT clonotypes (AA) (by default CDR3-IMGT lengths ≥4 AA and ≤45). In the right panel, 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 here is for “IMGT/HighV-QUEST set 1.”
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: IMGT/StatClonotype interface with its two panels. In the left panel, users choose the files of the two sets to be compared and can select the CDR3-IMGT length range of IMGT clonotypes (AA) (by default CDR3-IMGT lengths ≥4 AA and ≤45). In the right panel, 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 here is for “IMGT/HighV-QUEST set 1.”
Mentions: The IMGT/StatClonotype interface comprises two panels. In the left panel (Figure 1), users choose the files of the two IMGT/HighV-QUEST sets to be compared. These files correspond, for each set, to the file “stats_xxx” from the data directory of the IMGT/HighV-QUEST statistical output and have to be previously uploaded by the user. Users can select the CDR3-IMGT length range of IMGT clonotypes (AA) to be analyzed (by default CDR3-IMGT lengths ≥4 AA and ≤45). CDR3-IMGT length outliers are eliminated from the statistical procedure.

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.