Table 1.
Data summary of phosphorylation sites.
Fig 1.
Sequence (1D) and structural (3D and pure 3D) environments of globally phosphorylated serine sites represented by two sample logos and circular plots, respectively.
(A) Two sample logo of global PSSs in the PS1D-70 dataset. (B) Two sample logo of global PSSs in the PS3D-90 dataset. (C) 3D environments of global PSSs in the PS3D-90 dataset. (D) Pure 3D environments of global PSSs in the PS3D-90 dataset.
Fig 2.
Two sample logos of PSSs from the PS1D-70 dataset in different tissues.
Two sample logos of PSSs from the PS1D-70 dataset in perirenal fat (A), pancreas (B), testis (C), cortex (D), blood (E), stomach (F), liver (G) and heart (H). See data on other tissues in Figs C–T in S1 Supporting Figures.
Fig 3.
Sequence (1D) and structural (3D and pure 3D) environments of PSSs, PTSs, and PYSs from the PS3D-90 dataset represented by two sample logos and circular plots, respectively.
Data for brain and kidney is shown (see S1 Supporting Figures for all tissues). The circular amino acid propensity plots were produced by our in-house software tool. Color code for amino acid residue enrichment in the circular plots: (i) red–enriched, if p-value < 0.05 and odds ratio > 1, (ii) blue–depleted, if p-value < 0.05 and odds ratio < 1, and (iii) white–neither enriched nor depleted, if p-value ≥ 0.05.
Fig 4.
KEGG pathway analysis of the serine phosphorylated proteins from the PS1D-70 dataset.
Pathways with a corrected p-value < 0.01 in each tissue are considered significantly enriched. Insignificant results are represented by white color. Only the tissues with at least one significantly enriched pathway are shown.
Fig 5.
Tissue preferences of kinases targeting serine phosphorylated sites in the PS1D-70 dataset.
Tissues with a corrected p-value < 0.01 in each kinase class are considered significantly enriched for the corresponding kinase classes. Insignificant results are represented by white color. See S2 Data for corrected p-values.
Fig 6.
Comparison of the Ser/Thr kinase expression across tissues.
Expression values are colored in log scale. Kinases with a corrected p-value < 0.01 in each tissue are considered significant and are indicated with black circles. Grey rectangles represent kinases whose expression values could not be found in the downloadable dataset of the PaxDb database. Note that only the expression values of tissues drawn here could be found in the PaxDb database. The median value 8.671 is assumed as the midpoint, calculated from all expression values in this heatmap. See S2 Data for expression values and corrected p-values.
Fig 7.
Tripartite graph showing interactions between serine phosphorylation motifs, kinases and tissues.
The red parallelograms, yellow circles and green octagons represent kinases, motifs and tissues, respectively. Phosphorylated serine residues in motifs are represented with pS. Threonine and tyrosine phosphorylation sites are not shown in the network since no match between consensus kinase motifs and enriched tissue motifs was found.