Confounding effects of inferring gene co-expression networks from pooled data from different biological populations

Weighted Gene Co-expression Network Analysis (WGCNA) is routinely applied to pooled datasets from multiple biological populations, genotypes, or treatment groups, implicitly assuming a shared module structure across groups. While the distortion of pairwise correlations by pooling heterogeneous groups is well established statistically, three aspects of this problem have received little systematic attention in the context of co-expression network analysis: the extent to which pooling disrupts the discrete module-level community structure inferred by WGCNA; whether this disruption is detectable from the global topology metrics researchers routinely report; and how prevalent the pooling practice is in published multi-group WGCNA studies. Using analytical toy examples and a four-scenario simulation framework, we address all three questions. Module preservation Z _summary scores declined progressively with between-population divergence, from full preservation under identical populations (mean median Z _summary = 25.2 ± 3.3, 95% interval 19.0–30.7 across 20 simulation replicates) to substantial disruption when both network structure and mean expression differed (mean median Z _summary = 11.9 ± 1.0, 95% interval 10.2–13.5). This disruption was undetectable from global topology metrics: modularity and clustering coefficient remained stable across all scenarios, while edge density was sensitive but non-specific. These findings were corroborated in an empirical reanalysis of divergent lake and stream stickleback transcriptomes, where merged analysis collapsed 26 lake-specific and 59 stream-specific modules into only 19 merged modules. A survey of 100 publications found that 78.7% (95% CI 69.4–87.9%) of multi-group WGCNA studies with sufficient methodological reporting used a single merged analysis. Results were robust across network sizes of 250–1,000 genes and rewiring rates of 10–50%. We provide concrete recommendations including module preservation testing in both directions, population-specific baseline networks, and consensus WGCNA as a principled alternative.