Extended Data Fig. 2: Remodelling of cell model proteomes during adipogenesis.
(a) PCA of the adipogenic differentiation stages of the cell lines (depicted from light to dark) (filtering for a minimum of 5% valid values across all models, time points, and missing values imputed based on a normal distribution). (b) PCA loadings with the major driver proteins involved in lipid metabolism are shown in red. (c), (F), (I), and (L) PCAs of adipogenic differentiation stages of each cell model. (d), (G), (J), and (M) PCA loadings with the major driver proteins involved in lipid metabolism are shown in red for each cell model. (e), (H), (K), and (N) volcano plots for each cell model comparing the proteomes of preadipocytes and adipocytes from day 14 (n = 3, FDR < 10^(−2) and S0 = 0.1). The most strongly upregulated or downregulated proteins are indicated in orange and blue, respectively. (O) Number of proteins quantified during differentiation in each cell model (min. two detections in at least one time point), and the number of significantly regulated proteins or proteins exclusively quantified in either mature adipocytes or preadipocytes (two-sided Student’s t-test, FDR < 10^(−2)). (P) Enrichment analysis for GO-terms, keywords, and KEGG pathways among proteins of the stable proteome during adipogenesis (one-sided Fisher’s exact test, enrichment score >2, Benjamini-Hochberg FDR < 0,1).
