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. 2020 Mar 6;9:e54224. doi: 10.7554/eLife.54224

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© 2020, Kim et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 4. — (A) Diagram showing procedures for the identification of proteins with altered pTyr levels. (B) A volcano plot showing proteins with significantly up- or downregulated pTyr levels (fold change >1.5, p<0.05) in the cortex and hippocampus of Emx1-Cre;Ptprs^fl/fl (P21). Samples from three WT or KO mice were pooled for each analysis. Note that a single protein can be linked to multiple dots (different pTyr motifs); conversely, the same peptide can belong to two different proteins (e.g., Erbin and LRRC7). (C) Functional analysis (DAVID GO analysis) of proteins from Emx1-Cre;Ptprs^fl/fl mice with significantly altered pTyr levels. Note that synapse-related GO terms are strongly enriched. (D–F) Sunburst plots from SynGO analyses of specific pre- and postsynaptic localizations of proteins with altered pTyr levels (total, upregulated, and downregulated) from the Emx1-Cre;Ptprs^fl/fl cortex and hippocampus. Note that upregulated proteins tend to be those that localize to presynaptic sites, whereas downregulated proteins tend to be those that localize to postsynaptic sites. (G) Volcano plots showing that presynaptic proteins, determined by SynGO analyses, showed mainly increased pTyr levels, whereas postsynaptic proteins showed mainly decreased pTyr levels. (H) Largely normal synaptic levels of PTPσ-related proteins in the hippocampus of Emx1-Cre;Ptprs^fl/fl mice (3 weeks), as shown by immunoblot analyses of crude synaptosomes. (n = 6 mice for WT and cKO and for some, 6, five mice for WT and cKO, *p<0.05, ns, not significant, one-sample t-test).

Figure 4—figure supplement 1. — (A) Diagram showing procedures for the identification of proteins with altered pTyr levels. (B) A volcano plot showing proteins with significantly up- or downregulated pTyr levels (fold change >1.5, p<0.05) in the cortex and hippocampus of Emx1-Cre;Ptprs^fl/fl (P21). Samples from three WT or KO mice were pooled for each analysis. Note that a single protein can be linked to multiple dots (different pTyr motifs); conversely, the same peptide can belong to two different proteins (e.g., Erbin and LRRC7). (C) Functional analysis (DAVID GO analysis) of proteins from Emx1-Cre;Ptprs^fl/fl mice with significantly altered pTyr levels. Note that synapse-related GO terms are strongly enriched. (D–F) Sunburst plots from SynGO analyses of specific pre- and postsynaptic localizations of proteins with altered pTyr levels (total, upregulated, and downregulated) from the Emx1-Cre;Ptprs^fl/fl cortex and hippocampus. Note that upregulated proteins tend to be those that localize to presynaptic sites, whereas downregulated proteins tend to be those that localize to postsynaptic sites. (G) Volcano plots showing that presynaptic proteins, determined by SynGO analyses, showed mainly increased pTyr levels, whereas postsynaptic proteins showed mainly decreased pTyr levels. (H) Largely normal synaptic levels of PTPσ-related proteins in the hippocampus of Emx1-Cre;Ptprs^fl/fl mice (3 weeks), as shown by immunoblot analyses of crude synaptosomes. (n = 6 mice for WT and cKO and for some, 6, five mice for WT and cKO, *p<0.05, ns, not significant, one-sample t-test).