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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 CDR-IMGT lengths. “CDR-IMGT lengths” displays interactive bar graphs for the distribution of IMGT clonotypes (AA) (for IMGT clonotype diversity) or distribution of sequences assigned to IMGT clonotypes (AA) (for IMGT clonotype expression) for a given CDR-IMGT type. Bar graphs are interactive showing, for a given CDR-IMGT length, the number of IMGT clonotypes (AA) or number of sequences between brackets. The lists of CDR3-IMGT sequences of the IMGT clonotypes (AA), for a selected CDR3-IMGT length, are given per set in tables downloadable in csv files. Bar graphs are downloadable in PNG format.
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Figure 5: IMGT/StatClonotype CDR-IMGT lengths. “CDR-IMGT lengths” displays interactive bar graphs for the distribution of IMGT clonotypes (AA) (for IMGT clonotype diversity) or distribution of sequences assigned to IMGT clonotypes (AA) (for IMGT clonotype expression) for a given CDR-IMGT type. Bar graphs are interactive showing, for a given CDR-IMGT length, the number of IMGT clonotypes (AA) or number of sequences between brackets. The lists of CDR3-IMGT sequences of the IMGT clonotypes (AA), for a selected CDR3-IMGT length, are given per set in tables downloadable in csv files. Bar graphs are downloadable in PNG format.

Mentions: “CDR-IMGT lengths” (Figure 5) displays interactive bar graphs for sets 1 and 2 showing the distribution of the number of IMGT clonotypes (AA) (for IMGT clonotype diversity) or of the number of sequences assigned to IMGT clonotypes (AA) (for IMGT clonotype expression) per CDR-IMGT length for a given CDR-IMGT type (1, 2 or 3) (CDR-IMGT length and numbers between parentheses are visible hovering with the mouse). The distribution of the lengths of the CDR1-IMGT and CDR2-IMGT (encoded by the V gene) depends on the usage of the different V genes and subgroups, whereas the distribution of the lengths of the CDR3-IMGT (which result from the V-(D)-J rearrangement) characterizes the junction of the IMGT clonotypes. CDR-IMGT lengths and positions are based on the IMGT unique numbering for V domains (21).


IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST
IMGT/StatClonotype CDR-IMGT lengths. “CDR-IMGT lengths” displays interactive bar graphs for the distribution of IMGT clonotypes (AA) (for IMGT clonotype diversity) or distribution of sequences assigned to IMGT clonotypes (AA) (for IMGT clonotype expression) for a given CDR-IMGT type. Bar graphs are interactive showing, for a given CDR-IMGT length, the number of IMGT clonotypes (AA) or number of sequences between brackets. The lists of CDR3-IMGT sequences of the IMGT clonotypes (AA), for a selected CDR3-IMGT length, are given per set in tables downloadable in csv files. Bar graphs are downloadable in PNG format.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: IMGT/StatClonotype CDR-IMGT lengths. “CDR-IMGT lengths” displays interactive bar graphs for the distribution of IMGT clonotypes (AA) (for IMGT clonotype diversity) or distribution of sequences assigned to IMGT clonotypes (AA) (for IMGT clonotype expression) for a given CDR-IMGT type. Bar graphs are interactive showing, for a given CDR-IMGT length, the number of IMGT clonotypes (AA) or number of sequences between brackets. The lists of CDR3-IMGT sequences of the IMGT clonotypes (AA), for a selected CDR3-IMGT length, are given per set in tables downloadable in csv files. Bar graphs are downloadable in PNG format.
Mentions: “CDR-IMGT lengths” (Figure 5) displays interactive bar graphs for sets 1 and 2 showing the distribution of the number of IMGT clonotypes (AA) (for IMGT clonotype diversity) or of the number of sequences assigned to IMGT clonotypes (AA) (for IMGT clonotype expression) per CDR-IMGT length for a given CDR-IMGT type (1, 2 or 3) (CDR-IMGT length and numbers between parentheses are visible hovering with the mouse). The distribution of the lengths of the CDR1-IMGT and CDR2-IMGT (encoded by the V gene) depends on the usage of the different V genes and subgroups, whereas the distribution of the lengths of the CDR3-IMGT (which result from the V-(D)-J rearrangement) characterizes the junction of the IMGT clonotypes. CDR-IMGT lengths and positions are based on the IMGT unique numbering for V domains (21).

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.