De novo segmentation of tiling array data. (a) Segmentation accuracy for roots across ten discrete expression levels (see inset). Sensitivity is defined as the proportion of exonic probes contained in predicted segments relative to all annotated exonic probes, or the proportion of identified exon segments to all annotated exons. Specificity indicates how many predicted expressed probes or predicted exons are annotated as such. (b) Sensitivity and specificity of predicted exon segments for roots in comparison with annotated exons, plotted in a sliding window across 2,000 exons along chromosome 4 together with information on repetitive probes (window of 5,000 probes; see inset). The heterochromatic knob, the centromere and peri-centromeres are depicted below the x-axis (for other chromosomes, see Additional data file 5). (c) Proportion of predicted exon segments, high-confidence exon segments (see text for definition), and unannotated exon segments (high-confidence predictions that do not overlap with any annotated exon by at least 25 base pairs). Numbers are based on combined length of each class. (d) Proportion of sample-specific exon segments among all unannotated high-confidence predictions. (e) Examples of RT-PCR validation of predicted novel transcripts.
Laubinger et al. Genome Biology 2008 9:R112 doi:10.1186/gb-2008-9-7-r112