A Hub-protein based visualization of large protein-protein interaction networks.
According as the protein-protein interaction (PPI) data more increase, we need to optimally visualize them as network, in that describing the relationship among proteins is able to easily analyze biological processes happened in a cell. In this paper, to fast layout large-scale PPI networks, we proposed a method taking hub-proteins into consideration, which have more interactions than any other proteins in a network. In other words, it enforces two core parts of Walshaw's multilevel force-directed placement algorithm (MLFDP) to be modified. The modification is achieved by coarsening and expanding all neighboring proteins of hub-protein just once, whereas only two proteins in Walshaw's method. Our experiments show that the quality of layout is better optimal and time cost is reduced up to 63% in comparison with other methods.
Bang
SunLee
S
Electronics and Telecommunications Research Institute, 138 Gajeongno, Yuseong-gu, Daejeon, 305-700, Korea. slbang@etri.re.kr
Choi
JaeHun
J
Park
JongMin
J
Park
Soo-Jun
SJ
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface
D011506:Proteins