Supplementary Figure 4: Module preservation and replication.

(A) Module preservation (z-summary, x axis) as assessed in the 4 test datasets. Each row reports the preservation of a module in the 4 datasets. The red dashed line marks the “strongly preserved” threshold and the green dotted line marks the “moderately preserved” threshold (as defined empirically by Langfelder, PLOS Computational Biology 2011). (B) We assessed the replication of the trait to transcriptional measure associations, at the gene-level and module-level (see Supplementary material). To do so, we computed the correlation between vectors of module-to-trait association in our study and in the Zhang et al. study (shown by the red dotted line). We compared the observed correlation between module-trait vectors with gene level associations through resampling. The histogram shows the empirical distribution of correlation coefficient between vectors of gene-to-trait associations in the Zhang study and this study, where we select 47 random genes 10,000 times.