Fig. 1

Proteomic analysis of HCT-116 cells with and without SOX4 overexpression. a Experimental design of the proteomic analysis. HCT-116 cells were infected with virus-containing SOX4-overexpressing vectors Overexpression group (OE) or empty vectors Control group (C). The selected stable cells were then suspension-cultured for sphere formation. Three biological repeats were performed. Proteins isolated from spheres were subjected to nanoLC-RP-MS/MS analysis. b Workflow of data analysis. Three biological repeats (blue, yellow, and green) and two technical repeats (T1 and T2) were performed. The data that was observed in each group and all three biological repeats and the coefficient of variation was less than 30 % between two technical repeats were kept for further analysis. c The results of nanoLC-RP-MS/MS analysis. In total, 3654 unique proteins were identified with high confidence (false discovery rate < 1 %) in which 3100 proteins were identified with at least two peptide fragments. Among them, 3432 proteins were quantifiable in which 2978 proteins were quantifiable with more than two peptide fragments. 2587 out of 3654 proteins were seen in two technical runs indicating the highly reproducible results of this study