Figure 3

Five CMT-related network modules. The solid lines indicate the interactions between protein and protein. The oval shaped nodes mean proteins and the diamond shaped nodes represent proteins or DNAs depending on their role in interactions. The nodes with a highlighted border are DEGs or the proteins encoded by DEGs. The node color means the degree of the expression level of a gene in T-CMT as compared to that of T-control, where red means over-expression and blue means down-expression in the T-CMT. (A) The process of finding CMT-related network modules. The most over expressed protein in this module was the chromodomain helicase DNA-binding protein 3 (CHD3). CHD3 is one of the core subunits of Mi-2/NuRD complexes which is a novel regulator of DNA damage responses. (B) A modules showing proteins such as elastin (ELN), fibrilin 1 (FBN1) and fibrilin 2 (FBN2), which are related with elastic fiber formation. (C) A module showing over-expression of collagen fibrillogenesis, including tenacin (TNC), alpha-parvin (PARVA) and Type VI collagen A3. TNC is an extracellular protein that functions as an organizer of collagen fibrillogenesis. (D) A module showing that thrombospodins (THBS), which are regulators of collagen fibrillongenesis, are over-expressed. (E) A module showing microtubular dimerization, representing cytoskeletal rearrangement. S100A4 and Rho GTPase activating protein 1 (ARHGAP1) help microtubule to depolymerize if there is cellular strain, while septin 2, 6 and 7 work together to maintain microtubular polymerization.