Figure 5

Cyclin D1-specific deregulated genes are connected to focal adhesion and actin skeleton network. (A) The PPI network shows 81 proteins corresponding to deregulated genes from CCND1 siRNA-treated cells by at least 2-fold compared with control and their interacting proteins obtained from I²D database constitute a single connected network with 79 proteins. Target nodes positions reflect their interactions with pathway-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. Target genes/proteins whose expression is up-regulated or down-regulated (up/downward triangle nodes, respectively) and their interacting proteins (round nodes) are annotated by focal adhesion pathway (blue nodes, KEGG hsa4510), actin cytoskeleton organization and biogenesis (green nodes, GO:0030036), common proteins to both annotations (turquoise nodes), or none of the above (grey nodes). Two proteins, FLRT2 and TMPRSS2, are identified in I²D, but did not connect to the other nodes at depth of the presented network. (B) Collagen type IV migration is decreased in BxPC3 and HPAC cells stably expressing shD1_1 compared with control shNS. Representative plots are shown of two repeated experiments completed in duplicate. A significant difference, p < 0.05, in migration between treatments shNS and shD1 or shD3 for each cell line is indicated with an asterisk (*), or between a pair of treatments was indicated with a bracket and asterisks. (C) mRNA levels of CCND1 in PANC1 cells transfected with pBMN compared to pBMN_CCND1 vector are significantly increased, p < 0.05 (*). (D) Collagen type IV migration is significantly increased, p < 0.05, in PANC1 cells upon transient overexpression of CCND1. PPI network analysis was done using NAViGaTOR 1.13 ([26]; http://ophid.utoronto.ca/navigator).