JETTA was demonstrated on the GG-H arrays (Xu et al, PNAS, 2011) with human liver and muscle tissue samples. JETTA processed raw probe intensities, calculated gene/exon/junction expressions, and detected alternative splicing events between two tissues. For skipped exons, JETTA found 145 confident candidates, among which three were seleceted for verification and validated by RT-PCR.
Raw array data of liver and muscle samples was processed through GCBIN background modeling, median-scaling normalization and median-polish summarization. Alternative spcling events were detected by combined filtering of gene expression, DABG, MADS and MIDAS.
|Filtering||Description||#. Genes||#. Exons|
|Annotated alternative exons||15,873||165,586|
|DABG when over-expressed||<0.01||5,539||13,150|
|Junction supports||Supported by at least one juction satisfying the same MIDAS and DABG criteria||2,999||6,461|
|Average gene expression of each liver and muscle||> median of overall expression|
|gene expression fold change||<2|
|DABG when less expressed||>0.1||122||145|
145 exons of 122 genes were selected for skipping events by
Download the list of the skipped exons
Plotting examples: SLK, GARNL1, and VPS39
Three detected genes, GARNL1(Exon25, PsId:368373), VPS39(Exon23, PsId:593948) and SLK(Exon13, PsId:38999), were validated with RT-PCR.
The left figure shows normalized fold changes( log2(muscle/liver) ) of array and RT-PCR (black: exon, read: inclusion jucntion, green: exclusion junction). All three candidates also have large fold-changes in the PCR results. The gel experiment results verified it again (right figure).
R script and outputs
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