title: Network construction and structure detection with metagenomic count data.
abstract: BACKGROUND
  The human microbiome plays a critical role in human health. Massive amounts of metagenomic data have been generated with advances in next-generation sequencing technologies that characterize microbial communities via direct isolation and sequencing. How to extract, analyze, and transform these vast amounts of data into useful knowledge is a great challenge to bioinformaticians. Microbial biodiversity research has focused primarily on taxa composition and abundance and less on the co-occurrences among different taxa. However, taxa co-occurrences and their relationships to environmental and clinical conditions are important because network structure may help to understand how microbial taxa function together.
  
  
  RESULTS
  We propose a systematic robust approach for bacteria network construction and structure detection using metagenomic count data. Pairwise similarity/distance measures between taxa are proposed by adapting distance measures for samples in ecology. We also extend the sparse inverse covariance approach to a sparse inverse of a similarity matrix from count data for network construction. Our approach is efficient for large metagenomic count data with thousands of bacterial taxa. We evaluate our method with real and simulated data. Our method identifies true and biologically significant network structures efficiently.
  
  
  CONCLUSIONS
  Network analysis is crucial for detecting subnetwork structures with metagenomic count data. We developed a software tool in MATLAB for network construction and biologically significant module detection. Software MetaNet can be downloaded from http://biostatistics.csmc.edu/MetaNet/.
authors.affiliation: Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, 90048 CA USA.
authors.forename: Zhenqiu
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Statistics, The Ohio State University, Columbus, 43210 OH USA.
authors.forename: Shili
authors.initials: S
authors.lastname: Lin
authors.affiliation: Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, 90048 CA USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Piantadosi
keywords: Metagenomics data; Modules; Networks analysis