Nucleic Acids Research, 2012, Vol. 40, No. 6 2419 Figure 4. Splicing during cardiomyocyte differentiation. (A) The probe set ‘10509631’ of Capzb shows one of the highest SI during cardiomyocyte differentiation (CB compared to ES and EB). In contrast, the ﬂanking probe sets in all three cell lines show a similar GNI indicating that they are expressed equally (in relation to the individual gene expression). (B) The integrated genome browser revealed that ‘10509631’ is targeting an exon, which is skipped in the upper and included in the lower isoform. Literature search revealed that the longer isoform is known as cardiac and muscle speciﬁc (see text). Both genome maps display a region of Capzb. the largest difference (SI = 4.38, Figure 4A) was Capzb. As shown in the GAA’s genome browser, several isoforms of this gene are known (only two out of six isoforms are shown in Figure 4B). The differentially expressed probe set (probe set ID ‘10509631’) indicates that the longer isoform of Capzb1 was expressed in CB while the corres- ponding exon for this longer isoform was skipped in ES and EB, thus, generating Capzb2 (29). The knownAlt track and AceView also identiﬁed this splicing event as indicated by the GAA-generated expression table. In addition, the GAA detected tissue speciﬁcity of this splicing event using the exon array dataset. The signiﬁ- cantly higher expression values of this probe set were recorded for heart and muscle compared with nine other tissues. This ﬁnding is in agreement with the result in Ref. (29), which reported that Capzb1 is predominately expressed in muscle and cardiac tissue while the shorter form is present in non-muscle tissues. Another study found these two isoforms have distinct functions and cannot replace each other (30). Next, we reason that there should be a set of genes whose expressions do not change but create different isoforms with altered expression patterns during cardiomyocyte differentiation, in which we termed this phenomenon as ‘isoform switch’. To screen for such genes, the following criteria were used: exons with increasing or decreasing expression levels (SI > 0.5, P < 0.05) of unregulated genes with opposite thresholds (gene level fold-change < 0.5, P > 0.05). As a result, eight genes were selected (Figure 5A). To provide an evidence for such isoform switched genes, we validated the known cassette exon of Spna2 (Spectrin alpha 2) by reverse transcription polymerase chain reaction (RT– PCR) experiment (Figure 5B and C). Comparison between heart development and cardiomyocyte differentiation The comparison of heart development and cardiomyocyte differentiation using the same thresholds as described