title: Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network.
abstract: The Dialogue for Reverse Engineering Assessments and Methods (DREAM) project was initiated in 2006 as a community-wide effort for the development of network inference challenges for rigorous assessment of reverse engineering methods for biological networks. We participated in thein siliconetwork inference challenge of DREAM3 in 2008. Here we report the details of our approach and its performance on the synthetic challenge datasets. In our methodology, we first developed a model called relative change ratio (RCR), which took advantage of the heterozygous knockdown data and null-mutant knockout data provided by the challenge, in order to identify the potential regulators for the genes. With this information, a time-delayed dynamic Bayesian network (TDBN) approach was then used to infer gene regulatory networks from time series trajectory datasets. Our approach considerably reduced the searching space of TDBN; hence, it gained a much higher efficiency and accuracy. The networks predicted using our approach were evaluated comparatively along with 29 other submissions by two metrics (area under the ROC curve and area under the precision-recall curve). The overall performance of our approach ranked the second among all participating teams.
authors.affiliation: Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, 20892 MD USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.affiliation: Badger Technical Services, LLC, San Antonio, 78216 TX USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Gong
authors.affiliation: School of Computing, University of Southern Mississippi, Hattiesburg, 39406 MS USA.
authors.forename: Haoni
authors.initials: H
authors.lastname: Li
authors.affiliation: Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, 39180 MS USA.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Perkins
authors.affiliation: School of Computing, University of Southern Mississippi, Hattiesburg, 39406 MS USA.
authors.forename: Nan
authors.initials: N
authors.lastname: Wang
authors.affiliation: School of Computing, University of Southern Mississippi, Hattiesburg, 39406 MS USA.
authors.forename: Chaoyang
authors.initials: C
authors.lastname: Zhang
keywords: Dialogue for Reverse Engineering Assessments and Methods (DREAM); Gene regulatory network (GRN); Relative change ratio (RCR); Time-delayed dynamic Bayesian network (TDBN)