Dynamic progression of refined PPANs for HUVEC under TNFα stress. Time series refined PPANs under the TNFα stress from 0 to 3 hours are presented to monitor the dynamic properties of association progression. Positions of nodes are rearranged based on approximately up/down-stream relationships of the proteins. The general signaling proteins are shown as elliptic nodes; square nodes represent the receptor proteins and diamond nodes represent the possible negative regulator proteins. Dash gray lines represent the associations which are related to negative regulators. The levels of gene expression are indicated by the node color, in which the red color means the gene expression at that time is higher than its gene expression without TNFα treatment and the green color means the gene expression at that time is lower than its gene expression without TNFα treatment. The complete and pellucid time series diagrams from 0 to 8 hours are presented in Supplementary Figures [Additional file 5].