Supplemental Data Set 5. Expressed Intergenic Regions and NMD Impairment-Responsive ncRNAs and Pseudogenes.

(A) Differential gene expression data for all annotated ncRNAs based on the analysis described in Supplemental Dataset 1I. Separate display of ncRNAs differentially expressed (either up- or downregulated) in the indicated samples. (B) Differential gene expression of annotated pseudogenic transcripts based on the analysis described in Supplemental Dataset 1I. The matrix provides counts for genes and pseudogenes differentially expressed (p < 0.01) in the indicated NMD-impaired samples relative to their corresponding controls. (C) Expression of identified intergenic regions; listed are total read counts for the indicated subsets and regions. Significantly expressed intergenic regions are marked by an asterisk, colored in green are the regions analyzed in Figure 7D. Furthermore, information on the numbers of intergenic regions, which are more than twofold up- or downregulated in the indicated types of NMD impairments versus their corresponding controls, is indicated below the table. For more detailed information on data analysis see Supplemental Methods.