beyond element-wise interactions identifying complex interactions in biological processes超出element-wise交互识别在生物过程复杂的交互.pdfVIP

Beyond Element-Wise Interactions: Identifying Complex Interactions in Biological Processes 1. 2. 3 1,4 Christophe Ladroue , Shuixia Guo , Keith Kendrick , Jianfeng Feng * 1 Department of Computer Science and Mathematics, Warwick University, Coventry, United Kingdom, 2 Mathematics and Computer Science College, Hunan Normal University, Changsha, People’s Republic of China, 3 Laboratory of Behaviour and Cognitive Neuroscience, The Babraham Institute, Cambridge, United Kingdom, 4 Department of Computer Science and Mathematics, Warwick University, Coventry, United Kingdom and Centre for Computational System Biology, Fudan University, Shanghai, People’s Republic of China Abstract Background: Biological processes typically involve the interactions of a number of elements (genes, cells) acting on each others. Such processes are often modelled as networks whose nodes are the elements in question and edges pairwise relations between them (transcription, inhibition). But more often than not, elements actually work cooperatively or competitively to achieve a task. Or an element can act on the interaction between two others, as in the case of an enzyme controlling a reaction rate. We call ‘‘complex’’ these types of interaction and propose ways to identify them from time-series observations. Methodology: We use Granger Causality, a measure of the interaction between two signals, to characterize the influence of an enzyme on a reaction rate. We extend its traditional formulation to the case of multi-dimensional signals in order to capture group interactions, and not only element interactions. Our method is extensively tested on simulated data and applied to three biological datasets: microarray data of the Saccharomyce