Table 3.

Explored RNA-Seq data set (obtained from the CCLE website)

DataSet Name	Tumor Class Distribution	ENSEMBL IDs (Genes)
lymph_lung	173 Haematopoietic and Lymphoid Tissue	57,820
lymph_lung	188 Lung	57,820
large_upper	56 Large Intestine	57,820
large_upper	31 Upper Aerodigestive Tract	57,820

We created two data sets from the CCLE data set each with two tumor cell lines: Haematopoietic and Lymphoid Tissue-Lung (lymph_lung) tumors and Large Intestine-Upper Aerodigestive Tract (large_upper) tumors. The lymph_lung tumor pair was chosen as both classes had the greatest number of samples in the CCLE data set and we intended to explore the prevalence of DE in a larger data set. The large_upper tumor pair was chosen as both tumors affect the digestive system.