Two online analyze modules were equipped in CancerSCEM: Gene analyze module and Sample analyze module. The Gene module mainly focused on the 1) Whole expression profiles of a target gene in specified cancer single-cell sample, 2) Expression in different cell subtypes in the sample, 3) Gene expression correlation analyze in the specific sample, and 4) Expression comparison between different single-cell RNA-seq or TCGA bulk RNA-Seq datasets. The sample module included three analysis functions: 1) Cell component comparison between single-cell samples, 2) Cell-cell interaction network construction, and 3) Survival analysis based on TCGA bulk gene expression data and clinical survival data. Note: All the following gene expression in the Gene module were abbreviated as GE.

Gene	GE in Sample	GE in Subtypes	GE Correlation	GE Comparison

Sample ID

Clustering Visualization

UMAPTSNEUMAP

Immune Checkpoint

Other Gene

FeaturePlot colors

LightGreen,RedYellow,MediumBlueGray,DarkMagentaLightGreen,Red

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Sample	Cell Component Comparison	Cell Interaction	Survival Analysis

Sample1 ID

vs.

Sample2 ID

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