Table 1 Identification of mRNAs associated with epithelial- or mesenchymal-state as determined by analysis of CCLE and TCGA datasets derived from indicated cancer entities.

Cancer entity	Number of samples		Number of epithelial state-associated mRNAs		Number of mesenchymal state-associated mRNAs
Cancer entity	CCLE	TCGA	CCLE	TCGA	CCLE	TCGA
Colon adenocarcinoma	46	462	1311	2212	3247	2864
Breast invasive carcinoma	40	1095	3454	2604	2478	4485
Lung adenocarcinoma	106	515	2954	653	2075	1156
Pancreatic adenocarcinoma	21	178	754	3292	468	5344
Bladder urothelial carcinoma	22	408	969	3787	1815	4156
Prostate adenocarcinoma	n.a.	497	n.a.	2888	n.a.	3945
Head&Neck squamous cell cancer	n.a.	303	n.a.	2077	n.a.	4140
Shared EMT-associated mRNAs identified in all analyzed cancer types			131	42	70	323
Shared CCLE/TCGA EMT-associated genes			16		4

In the CCLE screen, epithelial-state associated mRNAs were defined as mRNAs that showed a significantly higher expression in epithelial-like cancer cell lines compared with mesenchymal-like cell lines. Mesenchymal-state associated mRNAs were defined as mRNAs that showed a significantly higher expression in mesenchymal-like cancer cell lines compared with epithelial-like cell lines. Significance was calculated by a Student’s t-test (p < 0.05 was considered significant). n.a., not analyzed. In the TCGA screen, epithelial-state associated mRNAs were defined as mRNAs that positively correlated with expression of the epithelial marker CDH1 (r > 0.1) and negatively correlated with expression of the mesenchymal marker VIM (r < −0.1). Mesenchymal-state associated mRNAs were defined as mRNAs that negatively correlated with expression of the epithelial marker CDH1 (r < −0.1) and positively correlated with expression of the mesenchymal marker VIM (r > 0.1).

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