Look into the distribution of each gene-coexpressing modules (GEM) and associate top weighted genes by selecting GEM in below dropdown menu. Left panel shows the UMAP, top 20 genes and distribution of the inquired GEM over cell subtypes. Right panel displays the dot plots of all useful GEMs of this major cell type.

Look into the nonlinear Sigmoid relationship between gene-coexpressing modules (GEM) and ligand -> receptor (LR) pair in our curated CRC Atlas (n=151). On the right panel, you can also find the Top 10 significant GEM-LR pairs for your search, ranked by RSE (residual standard error).

Conditional independence is an important concept in causal analysis, and in our setting, if a pair of highly correlated GEMs becomes independent when conditioning on a ligand -> receptor (LR) pair, the LR is likely involved in transmitting signal between cells expressing the GEMs. Finding a GEM X-LR-GEM Y triplet leads to the hypothesis depicted in below figure. Herein, we provide the triplet results that pass the conditional independence test. (choose at least one)

Choose GEM-X

Epi1 Epi10 Epi11 Epi12 Epi13 Epi14 Epi15 Epi16 Epi17 Epi18 Epi19 Epi2 Epi20 Epi21 Epi23 Epi24 Epi26 Epi3 Epi34 Epi35 Epi4 Epi40 Epi41 Epi43 Epi44 Epi45 Epi49 Epi5 Epi50 Epi55 Epi56 Epi57 Epi6 Epi62 Epi68 Epi7 Epi72 Epi74 Epi75 Epi77 Epi79 Epi8 Epi80 Epi81 Epi82 Epi9 Myeloid1 Myeloid10 Myeloid11 Myeloid12 Myeloid13 Myeloid14 Myeloid15 Myeloid16 Myeloid17 Myeloid18 Myeloid19 Myeloid2 Myeloid20 Myeloid21 Myeloid22 Myeloid23 Myeloid24 Myeloid25 Myeloid26 Myeloid3 Myeloid32 Myeloid33 Myeloid35 Myeloid4 Myeloid41 Myeloid42 Myeloid43 Myeloid47 Myeloid48 Myeloid5 Myeloid50 Myeloid52 Myeloid53 Myeloid54 Myeloid56 Myeloid57 Myeloid58 Myeloid59 Myeloid6 Myeloid62 Myeloid63 Myeloid68 Myeloid7 Myeloid71 Myeloid72 Myeloid73 Myeloid74 Myeloid77 Myeloid8 Myeloid84 Myeloid9 PlasmaB1 PlasmaB10 PlasmaB11 PlasmaB12 PlasmaB14 PlasmaB15 PlasmaB16 PlasmaB17 PlasmaB18 PlasmaB19 PlasmaB20 PlasmaB21 PlasmaB22 PlasmaB23 PlasmaB26 PlasmaB29 PlasmaB3 PlasmaB30 PlasmaB32 PlasmaB35 PlasmaB38 PlasmaB39 PlasmaB4 PlasmaB41 PlasmaB42 PlasmaB44 PlasmaB5 PlasmaB51 PlasmaB56 PlasmaB57 PlasmaB6 PlasmaB63 PlasmaB8 PlasmaB81 PlasmaB84 PlasmaB9 Stroma1 Stroma11 Stroma12 Stroma13 Stroma14 Stroma15 Stroma16 Stroma17 Stroma18 Stroma19 Stroma2 Stroma20 Stroma21 Stroma22 Stroma23 Stroma24 Stroma26 Stroma27 Stroma28 Stroma3 Stroma32 Stroma34 Stroma35 Stroma37 Stroma4 Stroma40 Stroma41 Stroma42 Stroma43 Stroma44 Stroma45 Stroma48 Stroma49 Stroma5 Stroma54 Stroma55 Stroma56 Stroma58 Stroma59 Stroma6 Stroma61 Stroma62 Stroma63 Stroma64 Stroma65 Stroma66 Stroma68 Stroma7 Stroma73 Stroma78 Stroma8 Stroma80 Stroma85 Stroma9 TNK1 TNK10 TNK11 TNK12 TNK13 TNK14 TNK15 TNK16 TNK17 TNK18 TNK19 TNK2 TNK20 TNK22 TNK23 TNK26 TNK29 TNK3 TNK32 TNK33 TNK35 TNK38 TNK4 TNK41 TNK42 TNK44 TNK5 TNK50 TNK51 TNK52 TNK56 TNK57 TNK6 TNK66 TNK67 TNK7 TNK8 TNK9

Choose Ligand -> Receptor

ALCAM -> CD6 BMP2 -> ACVR1 BMP2 -> BMPR2 CADM1 -> CADM1 CCL13 -> CCR2 CCL14 -> CCR1 CCL19 -> CCR7 CCL2 -> CCR2 CCL23 -> CCR1 CCL5 -> CCR1 CCL5 -> CCR5 CCL7 -> CCR1 CCL7 -> CCR2 CD274 -> CD80 CD274 -> PDCD1 CD28 -> CD80 CD34 -> SELL CD40 -> CD40LG CD40LG -> CD40 CD58 -> CD2 CD70 -> CD27 CD80 -> CD274 CD80 -> CD28 CD80 -> CTLA4 CD86 -> CD28 CD86 -> CTLA4 CDH1 -> CDH1 CDH5 -> CDH5 CLCF1 -> IL6ST CLCF1 -> LIFR COL1A1 -> CD44 COL1A1 -> ITGA1 COL1A1 -> ITGA10 COL1A1 -> ITGA11 COL1A1 -> ITGA3 COL1A1 -> ITGA9 COL1A1 -> ITGAV COL1A1 -> ITGB1 COL1A1 -> ITGB8 COL1A1 -> SDC1 COMP -> CD36 COMP -> CD47 COMP -> ITGAV COMP -> ITGB1 CSF1 -> CSF1R CSF3 -> CSF3R CTSG -> F2R CX3CL1 -> CX3CR1 CXCL10 -> CXCR3 CXCL11 -> CXCR3 CXCL12 -> ACKR3 CXCL12 -> CXCR4 CXCL13 -> CXCR5 CXCL16 -> CXCR6 CXCL9 -> CXCR3 EREG -> EGFR ESAM -> ESAM F11R -> F11R F11R -> JAM2 F11R -> JAM3 FASLG -> FAS FLT3LG -> FLT3 FN1 -> CD44 FN1 -> ITGA4 FN1 -> ITGA5 FN1 -> ITGA8 FN1 -> ITGAV FN1 -> ITGB1 FN1 -> ITGB3 FN1 -> ITGB7 FN1 -> ITGB8 FN1 -> SDC1 HLA-A -> CD8A HLA-DMA -> CD4 HLA-DRA -> CD4 HLA-F -> CD8A ICAM1 -> ITGAL ICAM1 -> ITGB2 ICAM2 -> ITGAL ICAM2 -> ITGAM ICAM2 -> ITGB2 ICAM3 -> ITGAL ICAM3 -> ITGB2 ICOSLG -> CD28 ICOSLG -> CTLA4 ICOSLG -> ICOS IFNG -> IFNGR1 IFNG -> IFNGR2 IL10 -> IL10RA IL10 -> IL10RB IL11 -> IL6ST IL15 -> IL15RA IL15 -> IL2RB IL15 -> IL2RG IL17A -> IL17RA IL18 -> IL18R1 IL18 -> IL18RAP IL1A -> IL1R1 IL1A -> IL1R2 IL1A -> IL1RAP IL1B -> IL1R1 IL1B -> IL1R2 IL1B -> IL1RAP IL23A -> IL12RB1 IL6 -> IL6R IL6 -> IL6ST INHBA -> ACVR1 INHBA -> ACVR1B INHBA -> ACVR2A INHBA -> ACVR2B INHBB -> ACVR1 ITGA4 -> VCAM1 ITGA9 -> VCAM1 ITGAL -> CD226 ITGAL -> ICAM1 ITGAM -> ICAM1 ITGB1 -> VCAM1 ITGB2 -> CD226 ITGB2 -> ICAM1 JAM2 -> ITGA4 JAM2 -> ITGB1 JAM2 -> JAM2 JAM2 -> JAM3 JAM3 -> ITGAM JAM3 -> ITGB2 JAM3 -> JAM2 JAM3 -> JAM3 LAMC3 -> CD44 LAMC3 -> ITGA1 LAMC3 -> ITGA7 LAMC3 -> ITGA9 LAMC3 -> ITGAV LAMC3 -> ITGB1 LTA -> TNFRSF14 LTA -> TNFRSF1A LTA -> TNFRSF1B MADCAM1 -> ITGA4 MADCAM1 -> ITGB7 NECTIN3 -> TIGIT NEGR1 -> NEGR1 NFASC -> CNTNAP1 OCLN -> OCLN OSM -> IL6ST OSM -> LIFR OSM -> OSMR PDCD1LG2 -> PDCD1 PDGFA -> PDGFRA PDGFA -> PDGFRB PDGFB -> PDGFRA PDGFB -> PDGFRB PDGFC -> PDGFRA PLEKHO2 -> PDGFRB PTPRC -> CD22 PTPRM -> PTPRM RELN -> ITGB1 SELE -> GLG1 SELL -> MADCAM1 SELP -> SELPLG SELPLG -> SELE SELPLG -> SELP SPN -> SIGLEC1 SPP1 -> ITGA4 SPP1 -> ITGA9 SPP1 -> ITGAV SPP1 -> ITGB1 SPP1 -> ITGB3 SPP1 -> ITGB5 TGFB1 -> TGFBR1 TGFB1 -> TGFBR2 TGFB2 -> TGFBR1 TGFB2 -> TGFBR2 TGFB3 -> TGFBR1 TGFB3 -> TGFBR2 TNC -> ITGA8 TNC -> ITGA9 TNC -> ITGAV TNC -> ITGB1 TNC -> ITGB3 TNF -> TNFRSF1A TNF -> TNFRSF1B TNFSF10 -> TNFRSF10D TNFSF13B -> TNFRSF13B TNFSF13B -> TNFRSF13C TNFSF13B -> TNFRSF17 TNFSF14 -> TNFRSF14 TNFSF4 -> TNFRSF4 TNFSF9 -> TNFRSF9 TSLP -> IL7R VCAM1 -> ITGA4 VCAM1 -> ITGB7 VEGFA -> FLT1 VEGFA -> KDR VEGFB -> FLT1 VWF -> ITGAV VWF -> ITGB3

Choose GEM-Y

Epi1 Epi10 Epi11 Epi12 Epi14 Epi15 Epi16 Epi17 Epi18 Epi19 Epi2 Epi20 Epi21 Epi22 Epi23 Epi24 Epi26 Epi3 Epi34 Epi35 Epi4 Epi40 Epi41 Epi43 Epi44 Epi45 Epi49 Epi50 Epi55 Epi56 Epi6 Epi64 Epi68 Epi7 Epi74 Epi75 Epi77 Epi79 Epi8 Epi80 Epi81 Epi82 Epi9 Myeloid1 Myeloid10 Myeloid11 Myeloid12 Myeloid13 Myeloid14 Myeloid16 Myeloid17 Myeloid18 Myeloid2 Myeloid20 Myeloid21 Myeloid22 Myeloid23 Myeloid24 Myeloid25 Myeloid26 Myeloid3 Myeloid32 Myeloid33 Myeloid35 Myeloid4 Myeloid41 Myeloid42 Myeloid43 Myeloid48 Myeloid5 Myeloid50 Myeloid52 Myeloid53 Myeloid54 Myeloid56 Myeloid57 Myeloid58 Myeloid59 Myeloid6 Myeloid62 Myeloid63 Myeloid68 Myeloid7 Myeloid71 Myeloid72 Myeloid73 Myeloid74 Myeloid77 Myeloid8 Myeloid84 Myeloid9 PlasmaB1 PlasmaB10 PlasmaB11 PlasmaB12 PlasmaB14 PlasmaB15 PlasmaB16 PlasmaB17 PlasmaB18 PlasmaB19 PlasmaB2 PlasmaB20 PlasmaB21 PlasmaB22 PlasmaB23 PlasmaB26 PlasmaB29 PlasmaB3 PlasmaB30 PlasmaB32 PlasmaB35 PlasmaB38 PlasmaB39 PlasmaB4 PlasmaB41 PlasmaB42 PlasmaB44 PlasmaB5 PlasmaB51 PlasmaB56 PlasmaB57 PlasmaB6 PlasmaB63 PlasmaB7 PlasmaB8 PlasmaB81 PlasmaB84 PlasmaB9 Stroma1 Stroma11 Stroma12 Stroma13 Stroma14 Stroma15 Stroma16 Stroma18 Stroma19 Stroma2 Stroma20 Stroma21 Stroma22 Stroma23 Stroma24 Stroma26 Stroma27 Stroma28 Stroma3 Stroma32 Stroma34 Stroma35 Stroma37 Stroma4 Stroma40 Stroma41 Stroma42 Stroma43 Stroma44 Stroma45 Stroma48 Stroma49 Stroma5 Stroma54 Stroma55 Stroma56 Stroma58 Stroma59 Stroma6 Stroma61 Stroma62 Stroma63 Stroma64 Stroma65 Stroma66 Stroma68 Stroma7 Stroma73 Stroma78 Stroma8 Stroma80 Stroma85 Stroma9 TNK1 TNK10 TNK11 TNK12 TNK13 TNK14 TNK15 TNK16 TNK17 TNK18 TNK19 TNK2 TNK20 TNK22 TNK23 TNK26 TNK29 TNK3 TNK32 TNK33 TNK35 TNK38 TNK4 TNK41 TNK42 TNK44 TNK5 TNK50 TNK51 TNK52 TNK56 TNK57 TNK6 TNK66 TNK67 TNK7 TNK8 TNK9

To deconvolute the bulk-RNAseq expression data using our curated GEM gene list, you will need to upload the gene expression in <.csv> format of which the rowname is gene symbol and colname is sample ID. The data is better deconvoluted if the input matrix is log2(TPM+1) or log2(FKPM+1).

Choose CSV File

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