Figure 1. The difference of design and interest between exon and junction probes. Exon probes (yellow = exon 1; dark blue = exon 2; red = exon 3; green = exon 4) are designed to quantify the expression of each individual exon. To study the splicing regulation of exon 3, the intensity of the red probe should be compared to that from the other probes. In the same way, any exon regulation could be studied (exon probe design is independent of the annotation of known splicing events). Junction probes (purple = exon 1–exon 2 junction; light blue = exon 2–exon 3 junction; brown = exon 3–exon 4 junction; orange = exon 2–exon 4 junction) are designed to quantify the expression of exon–exon junctions (i.e., local splicing pattern). To study the splicing regulation of exon 3, the intensities of “inclusion probes” (i.e., red, light blue and brown probes) should be compared to those from the “exclusion probe” (i.e., the orange junction probe). More probes are available to study exon regulation, but only for known splicing events; for example, there is no “exclusion probe” for exon 2 that is not known to be an alternative exon.

Figure 2. Visualization systems for the Affymetrix Exon Array data: example of the siPTB/nPTB effect on exon 15 of the KIAA0652 gene. Screenshots of visualization using Genomics Suite (Partek), BLIS (Biotique Systems) and EASANA (GenoSplice technology) are provided. For each scheme, a green rectangle indicates the position of exon 15 of KIAA0652, which is regulated by siPTB/nPTB. (a) Genomics Suite (Partek). (1) Structure of the gene according to RefSeq; (2) Splicing Index of each probeset, same scale than the gene scheme, blue = siPTB/nPTB and red = siCTRL; (b) BLIS (Biotique Systems). (1) Tracks corresponding to gene annotation from EnsEMBL and RefSeq; (2) Intensity of probesets in the six samples: the three first lines correspond to siCTRL and the three last lines to siPTB/nPTB; (c) EASANA (GenoSplice technology). (1) Options available to filter probes to be displayed according to their expression level and specificity (GC content, overlap with repeat regions, cross‐hybridization); (2) Exon/intron gene structure with alternative events in red (exon 15 is known to be a cassette exon); (3) Regulation at the probe level: each bar corresponds to one probe, color of bar corresponds to probe regulation (red =  upregulation and green = downregulation). The exon position is retrieved by the gray track. The green rectangle indicates the position of exon 15 of KIAA0652, which is regulated by siPTB/nPTB.