Extended Data Fig. 3: Changes in protein copy number and differences between the cell models.
(a) Supervised hierarchical clustering of the z-scored temporal profiles of ranked copy numbers of significantly changed proteins in at least three of the four models (n = 3, ANOVA conducted on copy numbers, FDR < 10^(−2)). (b) Supervised hierarchical clustering of z-scored temporal profiles of all cell models of a subset of (A) with conserved temporal profiles (Pearson correlation of z-scored temporal profiles in all inter-cell model comparisons >0). The copy numbers of all the four models are shown next to each other at each indicated time point. (c) Representative GO-annotations, KEGG pathways, and Keywords enriched in the indicated clusters are shown. Enrichment values and p values are depicted as bubble size and colour code, respectively (one-sided Fisher’s exact test, enrichment score >2, Benjamini-Hochberg FDR < 0,1). (d) and (e) PCAs of the adipogenic differentiation stages of the cell lines (depicted from light to dark) showing components 3 and 4. (f) and (g) Unsupervised hierarchical clustering of z-scored protein levels of significantly different proteins between preadipocytes and adipocytes on days 0 and 14 across the four cell models, respectively (n = 3, ANOVA, FDR < 0.01). Representative GO-annotations, KEGG pathways, and Keywords enriched in the indicated clusters are shown (one-sided Fisher’s exact test, enrichment score >2, Benjamini-Hochberg FDR < 0,1). P values and enrichment scores are indicated by bubble colour and size (h) PCA showing Components 3 and 7, separating cell models of male and female donors. (i) PCA loading showing the major driver proteins of Component 3 in red. (j) Heatmap of LFQ intensities of PPARγ targets on day 14 (n = 3).
