Cross-species network analysis identifies functionally conserved growth regulators. Leaf transcriptomes from Arabidopsis, maize, and aspen capturing active growth (i.e., cell proliferation and cell expansion) were used to generate co-expression networks for each species (grey solid lines in top panel represent co-expressed genes in each species). Cross-species expression conservation analysis revealed sets of triplets: orthologs, one from each species (thick black dashed lines in top panel), with highly overlapping gene co-expression “neighborhoods” (thin red dashed lines in top panel). In the depicted example, the genes A1 – P1 – M1 form a triplet (top panel). The authors identified the subset of triplets containing an experimentally-validated growth regulator from Arabidopsis, maize, or aspen. From this triplet subset, 82 Arabidopsis orthologs with peak expression during active growth were classified as growth regulators and used as guides to identify additional growth regulator candidates. Following a guilt-by-association approach, 2206 genes that were highly co-expressed with the guides were categorized as predicted growth regulators. In the depicted example, query gene A1 is co-expressed with A2, A3, A4, A5, and A6 (thin grey lines in middle panel). Among A1’s gene “neighbors”, A2, A5 and A6 are guides associated with a growth-related Gene Ontology term, cell division (red double lines in middle panel). Thus, A1 is classified as a predicted growth regulator (red arrow in middle panel). As proof-of-concept, the authors performed a detailed literature search that confirmed growth-related functions for 34 out of 61 (55.7%) of the top predicted growth regulators. Additionally, they performed mutant screening for nine of the top predicted growth regulators and observed leaf growth-related phenotypes for two of them (bottom panel). Together, these results validate the utility of cross-species network analysis for predicting bona fide growth regulators. Adapted from (Curci et al., 2022) Figure 1 and Figure 5C.