robust detection of hierarchical communities from escherichia coli gene expression data健壮的检测从大肠杆菌基因表达数据层次社区.pdfVIP

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data ˜ 1,2 1,2 3 1,2 Santiago Trevino III , Yudong Sun , Tim F. Cooper , Kevin E. Bassler * 1 Department of Physics, University of Houston, Houston, Texas, United States of America, 2 Texas Center for Superconductivity, University of Houston, Houston, Texas, United States of America, 3 Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America Abstract Determining the functional structure of biological networks is a central goal of systems biology. One approach is to analyze gene expression data to infer a network of gene interactions on the basis of their correlated responses to environmental and genetic perturbations. The inferred network can then be analyzed to identify functional communities. However, commonly used algorithms can yield unreliable results due to experimental noise, algorithmic stochasticity, and the influence of arbitrarily chosen parameter values. Furthermore, the results obtained typically provide only a simplistic view of the network partitioned into disjoint communities and provide no information of the relationship between communities. Here, we present methods to robustly detect co-regulated and functionally enriched gene communities and demonstrate their application and validity for Escherichia coli gene expression data. Applying a recently developed community detection algorithm to the network of interactions identified with the context likelihood of relatedness (CLR) method, we show that a hierarchy of network communities can be identified. These communities significantly enrich for gene ontology (GO) terms, consistent with them representing biologi