Figure 6.

Examples of Candidates from Splicing Index Analysis. Top panels show the p-values (dotted line) and fold-changes (blue bars) for the expression of individual probesets. The centre panels show the values normalized for overall difference in gene expression (SI). Bottom panels show the raw hybridization levels of each probeset. A) MADD – successful use of the splicing index. In this example, in the presence of an overall 3-fold gene expression difference between the samples, the SI factors out the expression difference and indicates three alternatively spliced probesets – 3329761, 3329771, and 33291783 – all of which have strong supporting RefSeq annotation evidence for alternative splicing. B) TYMS – a typical false positive, where differences in probe response levels close to the edges of the transcript suggest alternative isoform usage. Such results are often erroneous, resulting from non-uniform response of individual probesets to large (in this case ~20 fold) changes in gene expression. Note the elevated signal intensity (bottom panel) at the 5' end of the gene, suggesting saturation, and a reduced intensity at the 3' terminus, possibly to reduced amplification efficiency.

Bemmo et al. BMC Genomics 2008 9:529   doi:10.1186/1471-2164-9-529
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