MOESM3 of Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition

Additional file 3: Table S2. Time-course monitoring of phosphorylation site abundance changes during EMT. (A) Total list of identified and quantified phosphosites across five time points. Protein IDs refer to UniProt database. Mod site highlights the phosphorylated S/T or Y residue within protein amino acid (aa) sequence. Localization prob is the confidence score for site localization of the phosphorylation (1 means fully unambiguous). Sequence window highlights the 31 aa residue within protein. Phosphosite intensity is the raw intensity and the normalized log2 transformed phosphosite abundance adjusted based on protein abundance (average of biological replicates, n = 3). 0 min_S and 0 min_L refer to Fig. 1b. ANOVA p value describes the ANOVA p value of phosphorylation levels. Cluster number refers to Figure S4A (blank means the indicated phosphosite was not used for clustering); isClusterMember determines whether the protein belongs significantly to the cluster assigned; ‘is Kinase’ determines whether the protein belongs to kinome; ‘is related with histone PTMs’ determines whether the protein has been described with histone PTMs modifiers. (B) Kinases predicted by iGPS which are responsible for significantly regulated (p value < 0.05 based on triplicates) phosphopeptides at the indicated times after TGF-β stimulation. (C) Annotation for cluster phosphoproteins. (C) GO-BP (gene ontology biological processes) enrichment results for cluster phosphoproteins.