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

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

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.

Two-sided unpaired limma-moderated t-test is used.

Two-sided unpaired limma-moderated t-test is used.

Coloured dots represent clonal T cells of different clusters and grey dots represent nonclonal cells.

STARTRAC-dist to quantitatively describe tissue distribution.

STARTRAC-expa indices to quantitatively describe clonal expansion.

STARTRAC-migr indices to quantitatively describe migration.

STARTRAC-tran indices to quantitatively describe developmental transition/differentiation.

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.

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

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.

Two-sided unpaired limma-moderated t-test is used.