Here is the gene list, excel spreadsheet, and R Data object for varying subsets of differentially expressed genes (100,200,400)
First, significant differential expression results were extracted from DESeq2 by using an adjusted p-value threshold of .05
From the subset of genes whose p_adj < .05, I used varying log2FC thresholds to obtain N differentially expressed genes
The absolute log2FC thresholds to obtain N genes are:
N = 100, abs(log2FC) > 2.58 --
N = 200, abs(log2FC) > 1.911 --
N = 400, abs(log2FC) > 1.4555 --
I then took the union of the N differentially expressed genes with the 17 genes of interest present in GSE141593 to obtain the dataset for the network analyses, for a max of N + 17 genes per dataset.
Let me know if you have any questions. Thanks!