We analyzed the genome-wide gene expression profiles of the iPSCs, HLCs, and GTEx livers using SVD as described above for all genes expressed at minimum three log2 transformed fold changes across all samples included in our study. All gene expression quantifications were log2 transformed for fold change estimates then filtered to exclude genes with minimal FC < 3. The resulting gene expression matrices were then quantile normalized, wherein expression estimates of all genes per individual were ranked by magnitude and the ranks were transformed into normal distribution. Gene expression levels were scaled across all samples after merging the three datasets for analyses.
