Platform concordance and factors affecting it for genes represented on both ATH1 and tiling arrays. (a) Pearson correlation coefficients (PCCs) of expression estimates. (b) Box plots showing expression correlation for genes that were either categorized by the number of probes on tiling arrays or categorized by the total length of nonredundant sequence spanned by ATH1 probes. The boxes have lines at the lower quartile, median, and upper quartile values. Whiskers extend to the most extreme value within 1.5 times the interquartile range from the ends of the corresponding box. Box plots are based on genes represented on both the ATH1 and the tiling array, with the total number of genes per category on the respective platform indicated at the top.

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.

At-TAX online resources for gene expression analysis. (a) At-TAX gene expression estimates derived from tiling (right) and ATH1 arrays across all analyzed samples in TileViz. Included in this example is a gene not represented on the ATH1 array (red line). (b) Display of predicted expressed segments (middle) and raw hybridization signals (bottom) along the chromosome (top) in a generic genome browser.

Comparison of expression estimates on tiling and ATH1 array platforms. Scatter plot of expression estimates in (a) roots and (b) inflorescences. (c) Correlation between expression changes between roots and inflorescences. (d) CAT (correspondence at the top) plot for genes identified differentially expressed in roots and inflorescences. Proportion of genes in common is shown as a function of increasing size of subsets containing the n genes with the highest P values.

Analysis of genes represented only on tiling arrays. (a) Average or (b) maximum expression levels for all genes across all samples. (c) Expression values of genes with an apparent tissue-specific or stage-specific expression pattern across all samples. Twenty genes with the highest z scores and maximum expression in root, senescing leaf, inflorescence, or flowers are shown.

Non-polyadenylated transcripts. (a) Correlation between expression levels for polyA(+) and polyA(±) samples. (b) Proportion of unannotated transcripts found in common or exclusively in either polyA(+) samples and polyA(±) samples, respectively, as determined with two independent methods.