Figure 6.

Functional analysis of SWATH-MS data. (A) KEGG diagram of VEGF pathway regulation and changes in abundance of pathway members identified in our experiments. Heat shock protein beta-1 (HSPB1), serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform (PPP3CA), GTPase KRas (KRAS), mitogen-activated protein kinase 1 (MAPK1), and Ras-related C3 botulinum toxin substrate 1 (RAC1) were upregulated, whereas mitogen-activated protein kinase 14 (MAPK14) was downregulated at day 28 of BG differentiation in comparison to day 0. (B) Selected biological processes (GO) upregulated at day 14 and downregulated at day 28 of both differentiations. Log2 fold change comparison between day 0 and day 14 or 28 of S and BG differentiation with fold change ≥ 2 and p ≤ 0.05. (C) Upregulation and downregulation of selected terms in biological processes of the GO section in differentiated cells. Log2 fold change comparison between day 0 and day 28 of S and BG differentiation for selected GO biological processes with fold change ≥ 2 and p ≤ 0.05. Differentially expressed proteins were identified with Limma R package, and KEGG/GO annotations were mapped with R package EGSEA.