Figure 1
Differentially expressed TARs (DE-TARs). (A) The CCNB1 locus, a positive control for cell-cycle, illustrating the tiling array data analysis workflow employed. For each condition (in this case the cell-cycle phases G0, G1, S and G2), the raw tiling array signal intensities (Signal) in overlapping sliding windows of 200 nt were evaluated to see if the expression was significantly higher than a background distribution, using the TileShuffle algorithm with q<0.05. The background distribution was generated from 10,000 GC controlled permutations of the individual array’s signals. Overlapping windows of significant expression were summarized to intervals labeled H. Analogously, differentially expressed intervals were generated for each pairwise comparison of interest for all intervals designated H in at least one condition of the dataset. Difference signals in windows of the same size were evaluated for a significantly higher differential expression than a background of 100,000 difference shuffles, with q<0.005 and labeled DE-TAR intervals. Repeat masked intervals are missing in the array design due to the ambiguity of probes mapping to these regions. (*) Wiggle track scale bars indicate y-axis scales of (6,16), (0,10), (-3.5,3.5) and (-4,4) for the signal, z-score, differential signal and conservation, respectively. (B) Expression signal from (A) aggregated over all exons of CCNB1. Boxes indicate the median, first and third quantiles. Notches are placed at and approximate a robust 95% confidence interval. (C) Overlap in expressed nucleotides between STAT3, p53 and cell-cycle (CC) datasets for known coding exons (Gencode v12, UCSC genes, Ensembl and RefSeq) and bona fide non-coding intergenic TARs. (D) Overlap between the three datasets in differentially expressed nucleotides. CC, cell cycle; Chr, chromosome; DE-TAR, significantly differentially expressed TAR; IQR, interquartile range; kb, kilobase; MB, million base pairs; TAR, transcriptionally active region.