Figure 1
Non-protein coding RNA expression in bladder cancer. (a) Overall biotype distribution of non-protein coding transcript (i.e. lincRNAs, antisense RNAs, miRNAs, snoRNAs, snRNAs and miscRNAs) identified using Cufflinks and Cuffmerge and annotated according to Gencode v19. (b) Biotype distribution of the significantly differentially expressed non-protein coding genes using CuffDiff analysis. (c) Heat map of 89 significantly differentially expressed lincRNAs between normal urothelium and BC. Rows represent individual lincRNAs, columns represent individual tissue samples (sorted according to tumor stage as indicated). Yellow indicates up-regulation and blue indicates down-regulation. Genes are mean centered (black color) and normalized. LincRNAs selected for functional characterization are highlighted in red. *LncRNAs up/down regulated in the TCGA dataset (FClog2 > 0.15 or <−0.15, p < 0.01). (d) The expression of the five selected lincRNAs in normal (n = 8) urothelium compared to BCs (n = 72). Significance was tested using Student’s t-test. FPKM: Fragment Per Kilobase of exon per Million mapped reads.
