Supplemental Data Set 4. Categorization of NMD-Regulated and Reference Gene Sets into Functional Subgroups.

(A) Functional categorization of genes derived from the different subsets described in Figure 3B as well as all annotated genes based on the TAIR10 release and all genes displaying AS evidence based on our data (“all AS”). Furthermore, indicated subsets of cassette exon (CE)-containing genes were analyzed. Category bin and names and corresponding counts are listed.
(B) Combination of MapMan based functional classifications into different functional subgroups as shown in table on the left side. Numbers of genes falling into these combined categories for the indicated subsets are shown. Below each set, data are also displayed in pie charts. Hypergeometrical test for differential representation of the combined categories are provided for the individual subsets.
(C) Differential gene expression data for annotated splicing factors in NMD-impaired samples versus their respective controls based on the analysis described in Supplemental Dataset 1I. Furthermore, expression of the annotated, representative isoforms was analyzed in WT and lba1 upf3-1 using rQuant as described in Supplemental Methods.