According to our data, the puzzling fact that probesets for one gene may show variable expression profiles can be clarified when viewing the data at the protein level. Such genes are likely to involve alternative transcript variants which are constitutively different in expression levels. We looked at two genes as examples. Shown in Figure 2A , three probesets in GDS1277 dataset, 1448556_at, 1421382_at and 1451844_at, were mapped to the mouse Prlr gene (GeneID: 19116), with the first probeset correlating to protein IPI00321091, or PRL-R3, and the other two correlating to protein IPI00408593, or PRL-R2. The Prlr gene was reported to encode at least seven isoforms of prolactin receptor precursor in mouse [16] . The two probesets corresponding to the same protein IPI00408593, showed similar expression profiles as expected, with a PCC value of 0.6738 (P = 4.57e-6); while the probeset corresponding to another isoform, IPI00321091, showed a significantly different expression profile, with PCCs of 0.2530 and -0.0331 separately for 1421382_at and 1451844_at ( Figure 2A ). These data were consistent with the previous report that these two isoforms were predominantly expressed in liver and kidney, where PRL-R3 was highly expressed and PRL-R2 was weakly expressed [16] . We noticed that the shape of the expression curve of PRL-R3 seemed to be somewhat comparable to those of PRL-R2, although PRL-R3 probeset presented an overall higher expression level. These phenomena may suggest that PRL-R3 and PRL-R2 are partially co-regulated so that they show a comparable expression pattern, but they are expressed at different levels probably due to diverse roles of the regulatory elements.