Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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Center for Computational Systems Medicine
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Tissue samples summary

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Annotation details for different cell compartments

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Cell type statistics by disease state

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Cell type dynamics in malignant transformation

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Cell lineage trajectory inference

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TF regulatory network analysis

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Cell-cell interaction analysis

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Stemness, Senescence, Metaplasia and NeoTCR signature analysis

Tissue: Colorectum

Tissue samples summary

check button Cell type statistics by tissue samples.
EpitheliaImmuneStromal
Bar plot representation of the fraction of all Epithelial cells in each sample composed of each cell type for the integrated scRNA-seq datasets of Breast tissues. Each row represents a single sample, with each color representing a different cell type present in the sample.Bar plot representation of the fraction of all Immune cells in each sample composed of each cell type for the integrated scRNA-seq datasets of Breast tissues. Each row represents a single sample, with each color representing a different cell type present in the sample.Bar plot representation of the fraction of all Stromal cells in each sample composed of each cell type for the integrated scRNA-seq datasets of Breast tissues. Each row represents a single sample, with each color representing a different cell type present in the sample.
∗Bar plot representation of the fraction of all Epithelial, Immune and Stromal cells in each sample composed of each cell type for the integrated scRNA-seq datasets of Colorectum tissue. Each row represents a single sample, with each color representing a different cell type present in the sample.

check button Tissue summary table.
TissueDisease StateReplicatesEpithelia UMAPPMIDSourcePlatform
ColorectumFAPF007Projection

35726067

GSE201348

10X Genomics
ColorectumADJA014-C-201Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA002-C-010Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA001-C-207Projection

35726067

GSE201348

10X Genomics
ColorectumADJA001-C-124Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA002-C-106Projection

35726067

GSE201348

10X Genomics
ColorectumADJA001-C-223Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA002-C-204Projection

35726067

GSE201348

10X Genomics
ColorectumADJA014-C-111Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA015-C-203Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA015-C-204Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA014-C-040Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA002-C-201Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA002-C-203Projection

35726067

GSE201348

10X Genomics
ColorectumADJA015-C-008Projection

35726067

GSE201348

10X Genomics
ColorectumADJA015-C-208Projection

35726067

GSE201348

10X Genomics
ColorectumADJA014-C-114Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA014-C-043Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA001-C-202Projection

35726067

GSE201348

10X Genomics
ColorectumFAPA001-C-119Projection

35726067

GSE201348

10X Genomics
∗Projection of epithelial scRNA-seq cells from Colorectum diseased tissue samples into the manifold of normal tissue epithelial cells. Projected cells are colored by nearest normal cells in the projection and normal epithelial cells are colored gray.
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Annotation details for different cell compartments

check button Single-cell atlas of expresion.
UMAP representations and annotations of Epithelial cells in the integrated scRNA-seq data of the selected tissue.UMAP representations and annotations of Immune cells in the integrated scRNA-seq data of the selected tissue.UMAP representations and annotations of Stromal cells in the integrated scRNA-seq data of the selected tissue.
∗UMAP representations and annotations of Epithelial, Immune, Stromal cells in the integrated scRNA-seq data of Colorectum tissue. Colors represent cell types of each compartment.

check button Cell markers.
TissueMajor Cell TypeMinor Cell TypeFull NameMarkers
ColorectumEpiSTMStem-like cellsSMOC2,RGMB,SOX9,LGR5,OLFM4,ASCL2,CD44,CD166
ColorectumEpiCTCrypt top colonocytesOTOP2,MEIS1
ColorectumEpiEEEnteroendocrineCHGA,CHGB,TPH1
ColorectumEpiABSAbsorptive cellsALDOB,CA2,SI
ColorectumEpiSSCSerrated specific cellsGSDMB,GSDMD,IL18,RELB,MDK,RARA,RXRA,PDX1,S100P
ColorectumEpiASCAdenoma-specific cellsAXIN2,RNF43,EPHB2,CDX2
ColorectumEpiTACTransit amplifying cellsPCNA,MKI67
ColorectumEpiGOBGobletATOH1,MUC2,TFF3
ColorectumEpiTUFTuft POU2F3,SOX9
ColorectumEpiIMENTSerrated specific cellsSLC26A2,CA1
ColorectumEpiIMGOBImmature gobletKLK1,ITLN1,WFDC2,CLCA1,LRRC26,RETNLB,SPINK4,AGR2
ColorectumImmMASTMast cellsTPSAB1,CPA3,HDC,CTSG,TPSB2,MS4A2
ColorectumImmDCDendritic cellsHLA-DQA1,HLA-DQB1,CLEC10A,CLEC9A,FCER1A,CST3,CD1C
ColorectumImmNKNatural killer cellsKLRF1,SH2D1B,NCAM1,FCGR3A,GNLY,NKG7,GZMH,FGFBP2,CX3CR1,NCR1,NCR3,B3GAT1
ColorectumImmMACMacrophagesFOLR2,FABP3,PLA2G2D,ITGAM,ITGAX,CSF1R,CD68,CD163,THBD
ColorectumImmMONMonocytesCD14,CLEC9A,FCGR1A,LILRB2,CD209,CD1E,FCN1,VCAN
ColorectumImmILCInnate lymphoid cellsIL7R,KIT,IL2RA,NCAM1,GATA3
ColorectumImmBNNaive B cellsCD19,IGHD,IGLL1,CD27,CD38
ColorectumImmBMEMMemory B cellsPAX5,MS4A1,CD19,IGLL5,VPREB3,CD79A,CD79B,IGKC,CD74,HLA-DRA,CD37,CD22
ColorectumImmGCGerminal center B cellsSERPINA9,HRK,HTR3A,BCL6,CD180,FCRLA
ColorectumImmPLAPlasma cellsSSR4,IGLL5,IGLL1,AMPD1,IGHA1,IGHA2,JCHAIN,CD38,TNFRSF17,SDC1,IGHG1,MZB1
ColorectumImmCD4TNNaive CD4+ T cellsIL7R,SELL,CCR7,S100A4,TCF7
ColorectumImmTH17T-helper 17IL17A,CTSH,KLRB1,IL26
ColorectumImmTH1T-helper 1CXCL13,IFNG,CXCR3,BHLHE40,GZMB,PDCD1,HAVCR2,ICOS,IGFLR1,ITGAE
ColorectumImmTFHT follicular helperCXCR5,BCL6,ICA1,TOX,TOX2,IL6ST,MAGEH1,BTLA,ICOS,PDCD1,CD200
ColorectumImmTREGRegulatory T cellsBATF,TNFRSF4,FOXP3,CTLA4,LAIR2,IL2RA
ColorectumImmCD8TEXPProgenitor exhausted CD8+ T cellsPDCD1,IL7R,GPR183,NR4A3,REL,TCF7
ColorectumImmCD8TEXINTIntermediate exhausted CD8+ T cellsPDCD1,LAG3,CD101,CD38,CXCR6,TIGIT
ColorectumImmCD8TEREXTerminally exhausted CD8+ T cellsTOX,GZMB,ENTPD1,ITGAE,HAVCR2,CXCL13,PDCD1,LAYN,TOX,IFNG,GZMB,MIR155HG,TNFRSF9,ITGAE
ColorectumImmCD8TCMCentral memory CD8+ T cellsCCR7,SELL,IL7R,CD27,CD28,PRF1,GZMA,CCL5,GPR183,S1PR1
ColorectumStrENDEndothelial cellsPECAM1,PLVAP,VWF,CLDN5,FLT1,RAMP2,FAM110D,INHBB,NPR1,NOVA2,GPIHBP1,SOX17
ColorectumStrLYMENDLymphatic endothelial cellsPROX1,LYVE1,PDPN,PROCR,FLT4
ColorectumStrCFIBCrypt fibroblastsWNT2B,RSPO3,BMP7,MAP3K2,COL6A1,CD36,CD44,CBLN2,SPOCK1,ACSS3,FN1,COL3A1,BGN,DCN,POSTN,C1R,MMP2,FGF7,MME,CD47
ColorectumStrVFIBVillus fibroblastsWNT5B,BMP7,MAP3K2,COL6A1,CD36,CD44,CBLN2,SPOCK1,ACSS3,FN1,COL3A1,BGN,DCN,POSTN,C1R,MMP2,FGF7,MME,CD47
ColorectumStrMYOFIBMyofibroblastsSYT10,SOSTDC1,DES,TAGLN,MYH11,TPM4
ColorectumStrPERIPericytesPDGFRA,CSPG4,MCAM,COX4I2,KCNJ8,HIGD1B,NOTCH3,HEYL,FAM162B
ColorectumStrADIPOAdipocytesPPARG,FABP4,ADIPOQ,LEP,CD36,PLIN1
ColorectumStrPVAPost capillary venulesSELP,ZNF385D,FAM155A,GALNT15,MADCAM1
ColorectumStrMVAMicrovascular cellsPLVAP,CD36,DYSF,NRP1,SH3BP5,FABP5,VWA1,BAALC,PRSS23,RAPGEF4,APLN,HTRA1
ColorectumStrGLIAGlia cellsGFAP
ColorectumStrECMExtracellular matrixFBLN1,PCOLCE2,MFAP5
ColorectumStrINCAFIntermediate cancer-associated fibroblastsPDGFRA,POSTN,ID1,ID3
ColorectumStrICAFInflammatory cancer-associated fibroblastsTWIST1,WNT2,FAP,CXCL1,CXCL2,IL1B,IL6,HGF

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Cell type statistics by disease state

Stacked bar graph representation of the fraction of each epithelial cell type derived from samples with different Disease States in the integrated dataset of the selected tissue. Cells from each Disease State sample have a different color.Stacked bar graph representation of the fraction of each immune cell type derived from samples with different Disease States in the integrated dataset of the selected tissue. Cells from each Disease State sample have a different color.Stacked bar graph representation of the fraction of each stromal cell type derived from samples with different Disease States in the integrated dataset of the selected tissue. Cells from each Disease State sample have a different color.
∗Stacked bar graph representation of the fraction of each epithelial cell type derived from samples with different Disease States in the integrated dataset of Colorectum tissue. Cells from each Disease State sample have a different color.

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Cell type dynamics in malignant transformation

check button Colorectum (GSE201348)
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check button Colorectum (HTA11)
∗Fraction of cell type in each scRNA-seq sample plotted against position of the sample in the malignancy continuum for all cell types in Colorectum tissue. Samples are colored based on if they are derived from different Disease States. Cell fractions are computed by dividing the number of cells of a given cell type by the total number of cells in the compartment (epithelial versus immune versus stromal).
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Cell lineage trajectory inference

Disease StateEpitheliaImmuneStromal
HealthyTrajectory analysis of cells of epithelial compartment in Healthy-derived samples of Colorectum tissue by using scvelo package in Python.Trajectory analysis of cells of immune compartment in Healthy-derived samples of Colorectum tissue by using scvelo package in Python.Trajectory analysis of cells of stromal compartment in Healthy-derived samples of Colorectum tissue by using scvelo package in Python.
PrecancerSERTrajectory analysis of cells of epithelial compartment in SER-derived samples of Colorectum tissue by using scvelo package in Python.Trajectory analysis of cells of immune compartment in SER-derived samples of Colorectum tissue by using scvelo package in Python.Trajectory analysis of cells of stromal compartment in SER-derived samples of Colorectum tissue by using scvelo package in Python.
TATrajectory analysis of cells of epithelial compartment in FAP-derived samples of Colorectum tissue by using scvelo package in Python.
TVATrajectory analysis of cells of epithelial compartment in MSI-H-derived samples of Colorectum tissue by using scvelo package in Python.
CRCTrajectory analysis of cells of epithelial compartment in AD-derived samples of Colorectum tissue by using scvelo package in Python.Trajectory analysis of cells of immune compartment in AD-derived samples of Colorectum tissue by using scvelo package in Python.Trajectory analysis of cells of stromal compartment in AD-derived samples of Colorectum tissue by using scvelo package in Python.
∗RNA velocity maps for epithelial, immune and stromal compartments of Colorectum tissue with different disease states.

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TF regulatory network analysis

Disease StateEpitheliaImmuneStromal
HealthyHeatmap representation of significantly different TFs among all cell types of epithelial compartment in Healthy-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in Healthy-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in Healthy-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
ADJHeatmap representation of significantly different TFs among all cell types of epithelial compartment in ADJ-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in ADJ-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in ADJ-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
SERHeatmap representation of significantly different TFs among all cell types of epithelial compartment in SER-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in SER-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in SER-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
ADHeatmap representation of significantly different TFs among all cell types of epithelial compartment in AD-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in AD-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in AD-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
FAPHeatmap representation of significantly different TFs among all cell types of epithelial compartment in FAP-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in FAP-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in FAP-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
MSI-HHeatmap representation of significantly different TFs among all cell types of epithelial compartment in MSI-H-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in MSI-H-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in MSI-H-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
MSSHeatmap representation of significantly different TFs among all cell types of epithelial compartment in MSS-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in MSS-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in MSS-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
CRCHeatmap representation of significantly different TFs among all cell types of epithelial compartment in CRC-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of immune compartment in CRC-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.Heatmap representation of significantly different TFs among all cell types of stromal compartment in CRC-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python.
TF target networkTF target networkTF target network
∗Heatmap: Heatmap representation of significantly different TFs among all cell types of epithelial compartment in Healthy-derived samples of Colorectum tissue by comparing their average AUC by using pySCENIC in Python. Regulon specific score for each cell type is colored.
∗Network: TF target network created from Healthy-derived samples of Colorectum tissue using Top 50 predicted target genes of each regulon. Edge lengths are the inferred TF-target weightings.

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Cell-cell interaction analysis

Disease StateCell TypeCircleSourceTarget
HealthyABSThe cell-cell communications between each two interacting cell types in Healthy-derived samples of the selected tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in Healthy-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in Healthy-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.
ADIPOThe cell-cell communications between each two interacting cell types in Healthy-derived samples of the selected tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in Healthy-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in Healthy-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.
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Disease StateCell TypeCircleSourceTarget
ADJABSThe cell-cell communications between each two interacting cell types in ADJ-derived samples of the selected tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs. Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in ADJ-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in ADJ-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.
ADIPOThe cell-cell communications between each two interacting cell types in ADJ-derived samples of the selected tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs. Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in ADJ-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in ADJ-derived samples of the selected tissue. Each row represents the significant ligand and receptor gene pairs.
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Disease StateCell TypeCircleSourceTarget
SERABSThe cell-cell communications between each two interacting cell types in SER-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs. Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in SER-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in SER-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
ASCThe cell-cell communications between each two interacting cell types in SER-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs. Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in SER-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in SER-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
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Disease StateCell TypeCircleSourceTarget
ADABSThe cell-cell communications between each two interacting cell types in AD-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in AD-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in AD-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
ASCThe cell-cell communications between each two interacting cell types in AD-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in AD-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in AD-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
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Disease StateCell TypeCircleSourceTarget
FAPABSThe cell-cell communications between each two interacting cell types in FAP-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in FAP-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in FAP-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
ADIPOThe cell-cell communications between each two interacting cell types in FAP-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in FAP-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in FAP-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
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Disease StateCell TypeCircleSourceTarget
MSI-HABSThe cell-cell communications between each two interacting cell types in MSI-H-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in MSI-H-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in MSI-H-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
ASCThe cell-cell communications between each two interacting cell types in MSI-H-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in MSI-H-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in MSI-H-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
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Disease StateCell TypeCircleSourceTarget
MSSABSThe cell-cell communications between each two interacting cell types in MSS-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in MSS-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in MSS-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
ASCThe cell-cell communications between each two interacting cell types in MSS-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in MSS-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in MSS-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
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Disease StateCell TypeCircleSourceTarget
CRCABSThe cell-cell communications between each two interacting cell types in CRC-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in CRC-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in CRC-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
ADIPOThe cell-cell communications between each two interacting cell types in CRC-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source cell population in CRC-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its target cell population in CRC-derived samples of Colorectum tissue. Each row represents the significant ligand and receptor gene pairs.
∗The cell-cell communications between each two interacting cell types in different states-derived samples of Colorectum tissue. Different colors in the circle plot represent different cell groups and the edge width is proportional to the indicated number of ligand-receptor pairs.
∗Bubble plot of proportion to the communication probability in significant signaling pathways between this cell type and its source and target cell population. Each row represents the significant ligand and receptor gene pairs.
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Stemness, Senescence, Metaplasia and NeoTCR signature analysis

check button Developmental potential inference using CytoTRACE.
1_developmental_potential_in_Healthy.png shows the analysis results of stemness, senescence, and metaplasia signatures2_developmental_potential_in_SER.png shows the analysis results of stemness, senescence, and metaplasia signatures3_developmental_potential_in_AD.png shows the analysis results of stemness, senescence, and metaplasia signatures4_developmental_potential_in_FAP.png shows the analysis results of stemness, senescence, and metaplasia signatures
5_developmental_potential_in_MSI-H.png shows the analysis results of stemness, senescence, and metaplasia signatures6_developmental_potential_in_MSS.png shows the analysis results of stemness, senescence, and metaplasia signatures7_developmental_potential_in_CRC.png shows the analysis results of stemness, senescence, and metaplasia signatures
∗Ridge plots of CytoTRACE score distributions for epithelial cells.

check button Cellular senescence signature (for three compartments).
Disease StateEpitheliaImmuneStromal
HealthyComparisons for degree of cellular senescence of epithelial compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of immune compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of stromal compartment in Healthy-derived samples of Colorectum tissue.
SERComparisons for degree of cellular senescence of epithelial compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of immune compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of stromal compartment in Healthy-derived samples of Colorectum tissue.
ADComparisons for degree of cellular senescence of epithelial compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of immune compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of stromal compartment in Healthy-derived samples of Colorectum tissue.
FAPComparisons for degree of cellular senescence of epithelial compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of immune compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of stromal compartment in Healthy-derived samples of Colorectum tissue.
MSI-HComparisons for degree of cellular senescence of epithelial compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of immune compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of stromal compartment in Healthy-derived samples of Colorectum tissue.
MSSComparisons for degree of cellular senescence of epithelial compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of immune compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of stromal compartment in Healthy-derived samples of Colorectum tissue.
CRCComparisons for degree of cellular senescence of epithelial compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of immune compartment in Healthy-derived samples of Colorectum tissue.Comparisons for degree of cellular senescence of stromal compartment in Healthy-derived samples of Colorectum tissue.
∗Comparisons for degree of cellular senescence among epithelial, immune and stromal cell populations of Colorectum tissue with different disease states.

check button Metaplasia and damage response signature (for epithelial cells).
HealthySERAD
Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.
FAPMSI-HMSSCRC
Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.
∗Comparisons of Metaplasia-associated damage scores among epithelial cell subpopulations.

check button Neoantigen-specific TCR clonotypes (NeoTCR) signature.
Comparisons of CD4+ and CD8+ NeoTCR signature scores among different disease states.Comparisons of CD4+ and CD8+ NeoTCR signature scores among different disease states.
∗Comparisons of CD4+ and CD8+ NeoTCR signature scores among different disease states.