The direction of expression differences in case-control comparisons can be informative for interpretation and for generating hypotheses about potential risk and pathology mechanisms. I realize this information can be derived from the supplemental tables, but in the main text, it would be useful to include the direction of effect for the 962 genes with differentially expressed features. Are these differences predominantly due to reduced expression in BD, like the two highlighted modules, or are there some sets of genes with elevated expression in BD? Do the 41 overlapping genes between sACC and amygdala have the same direction of effect, and/or the same gene feature that is differentially expressed? To illustrate this directly, Figures 1 and 3 could potentially be expanded/modified to include information about the direction of effect for differentially expressed features.
[x] Generate volcano plots for each of the 4 features for each brain region as these will show significance, fold change and direction of effect
There are several packages for making volcano plots. A quick google search showed:
lcolladotor
commented
3 years ago
There are several packages for making volcano plots. A quick google search showed: