Figure 4

Cyclin D3-specific deregulated genes and their functional networks. A protein-protein interaction (PPI) network shows proteins corresponding to deregulated genes in CCND3 siRNA-treated cells and their interacting proteins obtained from I²D protein interaction database ver. 1.7 [23] annotated to the cell cycle process. Target genes/proteins whose expression is up-regulated or down-regulated (up/downward triangle nodes, respectively) by at least 2-fold compared with control and their interacting proteins (round nodes) are annotated by either GO cell cycle term (pink nodes, GO:0007049), KEGG cell cycle pathway (green nodes, KEGG hsa4110), common to both annotations (orange nodes), or none of the above (grey nodes). Target nodes positions reflect their interactions with cell cycle annotated nodes (colored), connecting directly to the annotated nodes or via intermediate node(s). Nodes and edges not directly connecting target nodes to pathway-annotated interacting nodes were faded out to reduce network complexity. This network incorporates 37/72 deregulated genes from CCND3 siRNA-treated cells; 36 proteins form a single connected network. A single target IFIT2 was identified in I²D, but did not connect to the other nodes at the depth of the presented network. PPI network analysis was done using NAViGaTOR 1.13 ([26]; http://ophid.utoronto.ca/navigator).