Tiling array data and sequence-based data give similar views of the transcriptome. (a) Gene intensities (left) and exon intensities (right) from the tiling data were binned at 0.1 increments of gene intensity (log2 scale) and compared with the intensities deriving from sequence data; there is a strong correlation (R2 = 0.95) between gene intensities derived from both technologies. YA, young adult.(b) Approximately 90% of the genes expressed based on tiling are also expressed in the sequence data in both stages sequenced. (c) Sample screenshot from Affymetrix Integrated Genome Browser illustrating how tiling array data and sequence data correspond to predicted gene structures. Tiling array data from four developmental stages (L3 and L4 larvae, YA and gravid adults (GA)) are shown in shades of blue. The predicted exons of unc-52 (ZC101.2) are shown at the top of the plot. Exons that are differentially spliced across development based on tiling data are shown in yellow. Regions corresponding to transfrags that do not overlap predicted exon structures are highlighted with purple bars. Sequence data for a single developmental stage (YA) is shown in red at the bottom of the figure; note that the regions identified as transcribed by sequencing correspond closely to those identified by tiling. Non-adjacent exon boundaries spanned by sequence reads are shown as green bars and the exons removed by the alternative splice shown in red below; the height of the green bar corresponds to the frequency with which the alternative splice events were detected.