Fig. 5: Functional annotation of differentially expressed proteins in different states of pluripotency.
From: The translational landscape of ground state pluripotency
a Gene ontology analysis of differentially expressed proteins in SL or EPI when compared to 2iL state. Two-sided P values were adjusted for multiple testing using Benjamin–Hochberg correction. b Examples of GO-term categories enriched in SL (focal adhesion) or in 2iL (glutathione metabolism). Differentially expressed proteins belonging to each category are shown. Upregulated proteins in SL or EPI are shown in red and upregulated proteins in 2iL are shown in blue. c Enrichment analysis for large protein complexes using differentially expressed genes between 2iL and SL/EPI. Two-sided P values are derived from the hypergeometric test associated with each protein complex and were adjusted for multiple testing using Benjamin–Hochberg correction. d Heat-map showing the fold change in protein expression for members of the top three enriched protein complexes from panel c and during 2iL to SL and EPI transition. e Single inhibitor withdrawal proteomics. 2iL cells were cultured for 1 and 3 days with serum-free medium supplemented with CH/LIF or PD/LIF and were employed in proteome analysis. Heat-map showing the change in protein expression for the 642 differentially expressed proteins between SL/EPI and 2iL. “C/P” refers to the proteins that require either PD or CH to maintain expression similar to 2iL ESCs; only removing both inhibitors from 2iL induces changes resembling the SL/EPI states. “2i” refers to the proteins that require both PD and CH signaling to maintain expression similar to 2iL state; removing either PD or CH from 2iL induces changes similar to SL/EPI state. “P” refers to the proteins that require PD to maintain an expression pattern similar to 2iL. “C” refers to the proteins that require CH to maintain an expression pattern similar to 2iL. n = 642 differentially expressed proteins. f The overlap between differentially expressed proteins regulated at the three levels and downstream of PD or CH single inhibitors.
