In a fold vs fold scatter plot the per gene log2 fold changes from two separate differential expression analysis are compared to each other. If the resultant plot shows a global correlation then it can be assumed that the biology is similar. Such plots can also be useful in identifying groups of genes with non correlating expression. Fold vs fold scatter plot are often considered a superior overlap method to Venn diagrams as they show the entire distribution of genes and so do not have a hard significance threshold.
