Figure 7

Disease-associated ncRNAs. The custom microarray was used with diffuse astrocytoma samples of different grades. (A) Principal component analysis for probes passing non-specific filtering. For at least four samples, the expression of the probe must be larger than the background, where background expression is defined by the mean intensities plus three times the standard deviation of negative control spots. The probe must have a non-specific change of expression of IQR>0.5. A separate principal components analysis was done for probes mapping to exons of known protein-coding genes (Gencode v12) and probes for which no evidence of short open reading frames was detected (see Materials and methods). The first two principal components accounted for 55% and 63% of overall variation, for probes mapping to exons of protein-coding genes and bona fide non-coding probes, respectively. (B) Number of bona fide non-coding DE-TARs either expressed in astrocytoma, i.e. overlapping at least one probe with an intensity larger than the background intensity for at least four samples, or differentially expressed in astrocytoma, i.e. overlapping at least one probe significantly differentially expressed between astrocytoma of grade I and aggressive states of grades III and IV (glioblastoma) (FDR<0.05). (C) Box plots depicting normalized log₂ intensities of all probes significantly regulated in astrocytoma (grade I compared to aggressive states, FDR<0.05) and located in the genomic loci of three selected macroRNAs, STAiR1, STAiR12 and STAiR2. Notches depict 95% confidence interval of the median intensity. Normalized log₂ intensities of a significantly regulated probe corresponding to SETBP1, a gene proximal to STAiR1, is shown next to the STAiR1 plot. (D) Overview of probe positions of probes located in the genomic loci of STAiR1, STAiR12 or STAiR2. CC, cell cycle; DE-TAR, significantly differentially expressed transcriptionally active region; GBM, glioblastoma; IQR, interquartile range; STAiR, STAT3-induced RNA; STAT3, signal transducer and activator of transcription-3.