Fig. 3

PPI network of bi-level regulated proteins constructed using an in-house tool. Nodes: The proteins with six-sector circle-shaped nodes were bi-level regulated proteins. In the circle nodes, the upper three sectors of the total six sectors represent the temperature condition that the protein was identified in the quantitative proteome study (from left to right; pink for high, light green for optimal, and blue for low temperature), and the lower three represent the temperature condition that the protein was identified in the phosphoproteome study (from left to right; orange for high, green for optimal, and cyan for low temperature). The cyan-bordered circle nodes indicate the up- or down regulated proteins with the expression level ≥ 1.5-fold, whereas the pink ones indicate the up- or down regulated proteins with the expression level < 1.5-fold compared to that of under the optimal condition. In the grey-bordered rectangular nodes, the leftmost pink strip indicates high temperature, and the rightmost blue strip indicates low temperature. All other proteins are indicated in black-bordered diamond-shaped nodes. Edges: The green edges indicate interaction-paths between bi-level regulated proteins (circle nodes), whereas the purple edges indicate interaction-paths between bi-level regulated proteins and differentially expressed proteins (rectangle nodes). Note: The protein SPLC1_S230960 does not have orthologous in Synechocystis sp. that is the template for PPI network construction of the in-house tool. Thus, there were no edges around its node, which is different from PPI network constructed by using STRING (see Additional file 12)