Fig. 3

Proteome and phosphoproteome analysis in PBML. (a) Proteome analysis of PBMCs at 6 am and 6 pm, significant proteins were determined using a t-test with permutation FDR. b PCA analysis of phosphosites at 6 am and 6 pm in RA and healthy subjects. c Volcano plot of the significant sites differing between 6 pm and 6 am in RA; significant sites were determined using the LIMMA package. d Sequence logo of significant sites between 06:00 and 18:00 found in RA. e Heat map showing the most significant time-of-day-regulated sites in RA only (peptide intensity levels shown [Z score]. Samples were scaled by row; clustered by row and column). f Kinase network in RA. Kinases with phosphosites regulated by time of day in RA only were analysed in String (V10) and cytoscape. Red nodes indicate identification from dataset and white nodes were inferred by the String (V10) software. Known regulatory sites are shown in grey