dream4 combining genetic and dynamic information to identify biological networks and dynamical modelsdream4结合遗传和生物网络和动态信息识别的动力学模型.pdfVIP

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models 1. 2. 3 1,2,4 Alex Greenfield , Aviv Madar , Harry Ostrer , Richard Bonneau * 1 Computational Biology Program, New York University Sackler School of Medicine, New York, New York, United States of America, 2 Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America, 3 Human Genetics Program, Department of Pediatrics, New York University Langone Medical Center, New York, New York, United States of America, 4 Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America Abstract Background: Current technologies have lead to the availability of multiple genomic data types in sufficient quantity and quality to serve as a basis for automatic global network inference. Accordingly, there are currently a large variety of network inference methods that learn regulatory networks to varying degrees of detail. These methods have different strengths and weaknesses and thus can be complementary. However, combining different methods in a mutually reinforcing manner remains a challenge. Methodology: We investigate how three scalable methods can be combined into a useful network inference pipeline. The first is a novel t-test–based method that relies on a comprehensive steady-state knock-out dataset to rank regulatory interactions. The remaining two are previously published mutual information and ordinary differential equation based methods (tlCLR and Inferelator 1.0, respectively) that use both time-series and steady-state data to rank regulatory