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).

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

tSNE plot dot size

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Columns in clustering table to show:

patient

sample

sampleType

stype

total_features

total_counts

size_factor

cyclePhase

invariantTCR

Cluster

nGene

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

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Gene Symbol

tSNE plot dot size

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

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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.

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Gene Symbol

Violin line width

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Please wait a moment if the figure is not shown here.

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

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Gene Symbol

Box plot line width

Box plot dot size

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

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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.

Gene Symbol1

Gene Symbol2

Gene1 low/hi exp cutoff

Gene2 low/hi exp cutoff

Select Group1 for DE analysis

Select Group2 for DE analysis

Limma adj.Pvalue

Limma logFC

Label logFC of G1 HEGs

Label logFC of G2 HEGs

Volcano dot size

Volcano label size

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

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.

Select Cluster1

Select Cluster2

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Limma adj.Pvalue

Limma logFC

Label logFC of C1 HEGs

Label logFC of C2 HEGs

Volcano dot size

Volcano label size

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.

Please wait a moment if the figure is not shown here.

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

Select Cell Type1

Select Cell Type2

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Limma adj.Pvalue

Limma logFC

Label logFC of C1 HEGs

Label logFC of C2 HEGs

Volcano dot size

Volcano label size

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.

Columns in CD4 T cell marker table to show:

Gene.ID

Gene.Symbol

F.statistic

F.adjusted.Pval

MeanExp.CD4_C01.CCR7

MeanExp.CD4_C02.ANXA1

MeanExp.CD4_C03.GNLY

MeanExp.CD4_C04.TCF7

MeanExp.CD4_C05.CXCR6

MeanExp.CD4_C06.CXCR5

MeanExp.CD4_C07.GZMK

MeanExp.CD4_C08.IL23R

MeanExp.CD4_C09.CXCL13

MeanExp.CD4_C10.FOXP3

MeanExp.CD4_C11.IL10

MeanExp.CD4_C12.CTLA4

Cluster

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Columns in CD8 T cell marker table to show:

Gene.ID

Gene.Symbol

F.statistic

F.adjusted.Pval

MeanExp.CD8_C01.LEF1

MeanExp.CD8_C02.GPR183

MeanExp.CD8_C03.CX3CR1

MeanExp.CD8_C04.GZMK

MeanExp.CD8_C05.CD6

MeanExp.CD8_C06.CD160

MeanExp.CD8_C07.LAYN

MeanExp.CD8_C08.SLC4A10

Cluster

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CD4 T cell marker table
CD8 T cell marker table

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

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Clonal frequency

tSNE plot dot size

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.

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

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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.

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Columns in TCR typing table to show:

Patient

Cell.name

T.cell.type

Cluster

Clone.ID

Clonal.status

Frequency

Identifier..Alpha1.

CDR3..Alpha1.

TPM..Alpha1.

Identifier..Alpha2.

CDR3..Alpha2.

TPM..Alpha2.

Identifier..Beta1.

CDR3..Beta1.

TPM..Beta1.

Identifier..Beta2.

CDR3..Beta2.

TPM..Beta2.

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TCR typing

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STARTRAC-dist to quantitatively describe tissue distribution.

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Ro/e cutoff1

Ro/e cutoff2

Ro/e cutoff3

Ro/e cutoff4

Ro/e is the ratio of observed cell number over the expected cell number of a given combination of T cell cluster and tissue.

Please wait a moment if the figure is not shown here.

STARTRAC-expa indices to quantitatively describe clonal expansion.

STARTRAC-migr indices to quantitatively describe migration.

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

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Box plot line width

Box plot dot size

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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.

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Box plot line width

Box plot dot size

Please wait a moment if the figure is not shown here.

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

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Please wait a moment if the figure is not shown here.

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.

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Box plot line width

Box plot dot size

Please wait a moment if the figure is not shown here.

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.

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Box plot line width

Box plot dot size

Please wait a moment if the figure is not shown here.

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

Cluster

CD4_C01-CCR7

CD4_C02-ANXA1

CD4_C03-GNLY

CD4_C04-TCF7

CD4_C05-CXCR6

CD4_C06-CXCR5

CD4_C07-GZMK

CD4_C08-IL23R

CD4_C09-CXCL13

CD4_C10-FOXP3

CD4_C11-IL10

CD4_C12-CTLA4

CD8_C01-LEF1

CD8_C02-GPR183

CD8_C03-CX3CR1

CD8_C04-GZMK

CD8_C05-CD6

CD8_C06-CD160

CD8_C07-LAYN

CD8_C08-SLC4A10

Cell Type

CD8 T cell

CD4 T cell

CD4+CD25- T cell

CD4+CD25+ T cell

CD4+CD25++ T cell

Tissue Type

Peripheral blood (P)

Adjacent normal (N)

Tumor-infiltrating (T)

Patient

P0123

P0215

P0309

P0411

P0413

P1228

P0701

P0825

P0909

P1012

P1207

P1212

Limma adj.Pvalue

Limma logFC

Labelling logFC of MSI HEGs

Labelling logFC of MSS HEGs

Volcano dot size

Volcano label size

adj.Pvalue represents Benjamini-Hochberg adjusted P-value. logFC represents log2(Fold Change). HEGs represents highly expressed genes.