Figure 3

Expression of both paralogs is generally detected in the same treatments, irrespective of the probe specificity (the degree to which each probe matches one but not the other paralog) or the detection threshold (the minimum raw intensity scored as expressed). These data are based on (A) "Standard" and (B) "Conservative" threshold levels for detection of expression and three probe specificities were compared that are labeled low, medium, and high (see Methods). We report paralogous profiles whose presence/absence scores in all five treatments were identical in the medium and high specificity analysis (shaded in gray on the left of each chart). 1789 and 1462 genes had consistent present/absent expression profiles in the medium and high specificity analyses using the standard and conservative thresholds. These sets of genes included 841 and 632 paralogous pairs, respectively. The tables on the right compare paralogous profiles by tabulating whether they are both present and absent in the same treatments (identical), the expression profile of one overlaps entirely with the other (overlap), or paralogs in which each duplicate has a unique component (distinct).