Figure S4 from Identification of Coding and Long Noncoding RNAs Differentially Expressed in Tumors and Preferentially Expressed in Healthy Tissues

Relative expression of several lncRNAs deregulated in LIHC in cell lines and liver tumors. A. Expression in cancer cells and fibroblasts. RNA was isolated from the indicated cells and the expression of the indicated lncRNAs was quantified by qRT-PCR. As a reference, the average expression of each lncRNA in all the liver cells evaluated is indicated as "average". The levels of RPLP0 mRNA were also evaluated and used as a reference to calculate the relative expression. The values indicate the average of 3 different experiments. Error bars denote standard deviations. A relative expression of 0.01 marks the lower detection limit. B. Expression in LIHC. The relative expression of each lncRNA was evaluated in paired peritumoral (PT) and tumor (T) samples from the TCGA RNA-Seq data. The result of the statistical analysis with paired t-tests is indicated in each graph. C. Analysis of RP11-242J7.1 expression in patients with different prognosis. Relative expression of RP11-242J7.1 in tumor and peritumoral samples of patients from the BCL-CUN cohort with best prognosis (Best; left) and worse prognosis (Worse, right). The result of the statistical analysis with Wilcoxon matched pairs signed rank tests is indicated in each graph. D. Analysis of lncRNAs associated with tumor differentiation (well versus poorly differentiated), tumor size (small versus large tumors) and with the number of tumor nodules (one versus multiple nodules) using data from the BCL-CUN cohort. The result of the statistical analysis (two-tailed unpaired t-test in B and U-Mann Whitney in C) is indicated in each graph.