Fig. 3

Proteome-wide expression in Mecp2 ^Jae/y cortex. a. Heat map of 460 significant, abundantly expressed proteins. Each column represents pooled biological replicates per genotype (n = 4), and each row represents the relative abundance fold change of an individual protein (with or without a PTM). Proteins with a p-value of < 0.1 were considered differentially abundant. b. Volcano plot of all the detected proteins’ expression (Log₂ fold change) in the Mecp2 ^Jae/y whole cortex proteome. Dotted line indicates a p-value of 0.1, where anything above the line indicates a significant protein. Previously identified RTT hits are highlighted in red, blue, or purple filled circles. Red circles denote that the significant protein was identified from a transcriptome-based gene expression study, blue circles denote identification from a proteomics-based study, and purple circles denote identification from a non-omics-based study. Due to space constraints, only the selected RTT protein hits identified from proteomics and non-omics-based studies were highlighted in this volcano plot. For a comprehensive list of all the identified RTT protein hits, refer to Additional file 8. c. Pie chart of significant proteins compared to top 500 cell type-specific genes based on the Zhang et al. study [69]. All significant proteins were included in the analysis. Each pie slice lists the number of significant proteins associated with each CNS cell type