Fig. 3

Characterization of functional modules impacted by reduced abundance of Caz, Smn and TBPH proteins. A Left panel: workflow used to generate and select functional modules. The adult brain interactome was obtained from the APID protein-interaction network after filtering for proteins expressed in the adult Drosophila brain (i, see Methods). Functional enrichment analysis of the resulting interactome was performed to retrieve overrepresented GO Biological Processes (ii). Note that the functional enrichment returns all the proteins annotated in each overrepresented term. The modules were generated from the functional enrichment by retaining the proteins annotated and simultaneously interacting in the brain network (iii). Finally, the impact of caz, Smn and TBPH knockdown was evaluated for each module (iv) to select modules with > 20% of transcripts altered in each individual knockdown (v). Right panel: summary the workflow outputs. “Overall impact” calculation is exemplified for two modules (X/Y) with the impact score indicated on the right. Only the Y module would be selected, as the overall impact of module X is below the defined threshold. B Line plot comparing the impact of individual knockdowns on selected modules, sorted by increasing overall impact. Modules with the highest impact for each protein are indicated by their short name. C Box plots showing the percentage of proteins with MND-linked orthologs in each module class. Selected modules (blue) are significantly enriched in proteins with MND-linked orthologs compared to non-selected modules (grey) (p value = 1.5e-3, Wilcoxon test). D Pie charts representing the fraction of transcripts with altered expression (DE) or splicing (AS) in response to a given protein knockdown that are simultaneously found in RNP complexes bound by the same protein. The high percentage of DE/AS transcripts (selected modules, blue pie chart) is significantly related to a higher frequency of DE/AS transcripts involved in RBPs bound by the same proteins (p-value = 5.4e-3, Chi² test of independence)