Gene Expression Matrices

Due to the huge volume of raw sequencing data, CancerSCEM didn't provide the download of raw reads, but provided the corresponding download link to the original database (see 'Original Metadata').
Here, to meet the needs of user for downstream personalized analysis, the normalized gene expression matrix for each cancer single-cell RNA-Seq dataset could be downloaded in a standard format (.tsv).

Cell Components and Differential Expression Genes

For each cancer single-cell sample, we provided the detailed statistics of the subtypes of immune cells and other cell types. For each subtype, the differential expression gene list was also provided for download, user can use it to do some personalized analysis.

Key Molecules Used in CancerSCEM

CancerSCEM has collected hundreds of functional molecules including receptor genes, ligand genes, oncogenes and tumor suppressor genes from numerous data sources like CelltalkDB, SingleCellSingalR, Cellinker, Cell-Cell Interaction Database, Cancer Gene Census, OncoKB, Network of Cancer Genes, TSGene, IntOGene, etc. The general analysis page only displayed the expression of those genes supported by three or more sources, while the complete gene lists were available for download.

Cell Interaction Calculated by CellphoneDB

The calculated results from CellphoneDB were provided for downloading. It mainly included three important files: 1) the file 'means.txt' represented the total average expression of each ligand-receptor pair in each cell-type pair; 2) 'pvalues.txt' meant the enrichment significance of each ligand-receptor pair in each cell-type pair; 3) 'count_network.txt' was the final count evaluation of interaction network for the given sample.