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Suppose there is an experiment designed to detect transcripts showing differential expression in two tissue groups: liver vs muscle. The alt-splicing ANOVA dialog allows you to specify the ANOVA model that in this analysis is the Tissue. The alt-splicing factor is chosen from the ANOVA factor(s), so the alt-splicing factor is also Tissue (Figure 1).  

The alt-splicing range will limit analysis to genes possessing the number of transcripts in the specified range. Lowering the maximum number of transcripts will increase the speed of analysis.

 

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SubtitleText Alt-splicing ANOVA comparisons setup dialog AnchorName Alt-splicing-contrast

Click Next to setup the comparisons (Figure 2). The levels (i.e. subgroups) of the alt-splicing factor will be displayed in the left panel; click to select a level name and move it to one of the panels on the right. The fold change calculation on the comparison will use the group in the top panel as the numerator, and the group in the bottom panel as the denominator. Click on Add comparison button to add a comparison to the comparisons table.

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For this analysis, only genes with more than one transcript will be included in the calculation. The report format is the same as ANOVA report, each row represent a transcript, and besides statistics information on the specified comparisons, there is also alt-splicing information at the right end of the table. That information is represented by the p-value of interaction of transcript ID with alt-splicing factor. Note that the transcripts of the same gene should have the same p-value. Small p-value indicates significant alt-splicing event, hence the table is sorted based on that p-value by default (Figure 4).

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