title: Investigating microbial co-occurrence patterns based on metagenomic compositional data.
abstract: BACKGROUND
  The high-throughput sequencing technologies have provided a powerful tool to study the microbial organisms living in various environments. Characterizing microbial interactions can give us insights into how they live and work together as a community. Metagonomic data are usually summarized in a compositional fashion due to varying sampling/sequencing depths from one sample to another. We study the co-occurrence patterns of microbial organisms using their relative abundance information. Analyzing compositional data using conventional correlation methods has been shown prone to bias that leads to artifactual correlations.
  
  
  RESULTS
  We propose a novel method, regularized estimation of the basis covariance based on compositional data (REBACCA), to identify significant co-occurrence patterns by finding sparse solutions to a system with a deficient rank. To be specific, we construct the system using log ratios of count or proportion data and solve the system using the l1-norm shrinkage method. Our comprehensive simulation studies show that REBACCA (i) achieves higher accuracy in general than the existing methods when a sparse condition is satisfied; (ii) controls the false positives at a pre-specified level, while other methods fail in various cases and (iii) runs considerably faster than the existing comparable method. REBACCA is also applied to several real metagenomic datasets.
  
  
  METHODS
  The R codes for the proposed method are available at http://faculty.wcas.northwestern.edu/∼hji403/REBACCA.htm
  
  
  BACKGROUND
  hongmei@northwestern.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Yuguang
authors.initials: Y
authors.lastname: Ban
authors.affiliation: Interdisciplinary Program in Statistics, University of Arizona, Tucson, AZ 85721, USA and Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Lingling
authors.initials: L
authors.lastname: An
authors.affiliation: Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Hongmei
authors.initials: H
authors.lastname: Jiang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007114:Immunization; D056186:Metagenomics / Q000379:methods*; D012867:Skin / Q000276:immunology / Q000382:microbiology* / Q000503:physiopathology*; D013045:Species Specificity