Fig. 3

The C. elegans body muscle transcriptome. A Left panel: heat map showing the body muscle expression levels log(fpkm) of the 20,362 protein-coding genes in WS250. a, BN452 positive control; m, body muscle transcriptome sample. The body muscle-specific transcriptome is highlighted with a dashed yellow line. Right panel: several examples of expression levels in genes identified in (a) BN452 (ubiquitously expresses GFP and mCherry in all nuclei; positive control) and (m) body muscle-specific nuclear fractions. The vertical axes mark expression levels as the log(FPKM). The body muscle-specific genes unc-54, mlc-1, unc-27, and lev-11 were all detected in our study, while the intestine-specific elt-2 and the GABA neuron-specific unc-47 were not present. (a: median log(fpkm) of the “BN452 all nuclei” dataset; m: median fpkm values of set1 and set2 muscle datasets). B The C. elegans body muscle interactome. We clustered all 2848 protein-coding genes identified in this study using previously published protein-protein interaction data. Each gene is shown as a pink dot. Within this network, we identified six smaller, highly interconnected subnetworks shown in different colors. The genes in each subnetwork were independently subjected to GO term enrichment analyses shown with colored panels above each respective subnetwork