Online data analyzer

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All T cells showing 20 major clusters (8 for CD8+ T cells and 12 for CD4+ T cells).

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Each dot represents one single cell, coloured by the expression level of selected gene.

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Violin plots showing the expression distribution of selected gene in T cell clusters. Box plots inside indicate quartiles, with horizontal lines representing median values and whiskers extending to the farthest data point within a maximum of 1.5×interquartile range.

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Box plots showing the expression distribution of selected gene in T cell clusters. Each dot represents one single cell, coloured by T cell clusters.

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Expression distributions of two selected genes.
Cell density is colour-coded, with red denoting high density and yellow low density.
The percentage and cell number of each subgroup are labeled in the corners.
low/hi exp cutoff represents the threshold defining low expression or high expression. DE represents differential expression. G1 represents selected Group1 and G2 represents selected Group2.

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Two-sided unpaired limma-moderated t-test is used.
adj.Pvalue represents Benjamini-Hochberg adjusted P-value. logFC represents log2(Fold Change). HEGs represents highly expressed genes. C1 is selected Cluster1 and C2 is selected Cluster2.

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Two-sided unpaired limma-moderated t-test is used.
adj.Pvalue represents Benjamini-Hochberg adjusted P-value. logFC represents log2(Fold Change). HEGs represents highly expressed genes. C1 is selected Cell Type1 and C2 is selected Cell Type2.
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Coloured dots represent clonal T cells of different clusters and grey dots represent nonclonal cells.
Clonal frequency is the number of cells harbouring same TCRs.

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Each row represents one clonotype, and each column represents one cluster in specific tissue. Heatmap value represents the number of cells harbouring the clonotype in the cluster of specific tissue.

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Bar plots showing the number of clonotypes and clonal cells in each T cell cluster. The clonotypes are categorized as unique (n = 1) and clonal (n = 2 and n ≥ 3) based on the cell numbers they harboured. Clonal cells are defined as those clonotypes containing at least two cells.
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STARTRAC-dist to quantitatively describe tissue distribution.
Ro/e is the ratio of observed cell number over the expected cell number of a given combination of T cell cluster and tissue.

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STARTRAC-expa indices to quantitatively describe clonal expansion.
STARTRAC-migr indices to quantitatively describe migration.
STARTRAC-tran indices to quantitatively describe developmental transition/differentiation.

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Pairwise STARTRAC-migr indices to quantitatively describe migration between different tissues.
N-P represents between adjacent normal tissue and peripheral blood.
N-T represents between adjacent normal and tumour tissues.
P-T represents between peripheral blood and tumour tissue.

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Pairwise STARTRAC-tran indices to quantitatively describe developmental transition/differentiation between different clusters.

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Kruskal Wallis test is used to compare cell percentages of MSI- with MSS-patients.
Box plots, centre lines represent median values; whiskers represent 1.5× interquartile range.

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Kruskal Wallis test is used to compare STARTRAC-indices of MSI- with MSS-patients. Box plots, centre lines represent median values; whiskers represent 1.5× interquartile range.

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Two-sided unpaired limma-moderated t-test is used.
adj.Pvalue represents Benjamini-Hochberg adjusted P-value. logFC represents log2(Fold Change). HEGs represents highly expressed genes.