Supplementary Figure 1: Enrichment of shared Gene Ontology (GO) terms and similar expression profiles in interacting protein pairs compared to control networks generated by replacing the prey proteins with random proteins from the search space.

(a) GO similarity scores for interacting protein pairs identified using the AD-cDNA library. Semantic similarity scores for the BP component of GO were calculated using the HRSS software package, which scores protein pairs on a scale of 0 (dissimilar GO terms) to 1 (similar GO terms)²⁹. (b) Same as (a), but for interactions identified using the AD-Fragment scores. Due to the already high semantic similarity scores for pairs in the search space (749 genes involved in early embryonic development), enrichment scores are less high than for AD-cDNA derived interactions. Control network bars represent the mean of 100,000 control networks ± s.d. Statistical significance is the fraction of control networks that displayed the same or higher fraction of pairs with a particular GO similarity range as the actual interaction network. Protein pairs in the interaction network are depleted for pairs with a low semantic similarity score, and enriched for pairs with a high similarity score. (c–f) Average Pearson correlation coefficient (PCC) score of mRNAs corresponding to protein pairs in the indicated interaction datasets (red arrows), compared with the distribution of average PCC scores of 100,000 control networks generated by replacing the bait proteins with random proteins from the search space (blue line). PCC values were calculated using the compendium of expression microarray data collected in Wormbase release WS236. Statistical significance is the fraction of control networks that displayed an average PCC score identical or higher than the actual interaction network. As observed previously⁹, early embryogenesis genes already have such similar expression profiles that no further enrichment can be observed for interactions derived from the AD-Fragment library.