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Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data

Author

Listed:
  • Patricio S La Rosa
  • Berkley Shands
  • Elena Deych
  • Yanjiao Zhou
  • Erica Sodergren
  • George Weinstock
  • William D Shannon

Abstract

Human microbiome research characterizes the microbial content of samples from human habitats to learn how interactions between bacteria and their host might impact human health. In this work a novel parametric statistical inference method based on object-oriented data analysis (OODA) for analyzing HMP data is proposed. OODA is an emerging area of statistical inference where the goal is to apply statistical methods to objects such as functions, images, and graphs or trees. The data objects that pertain to this work are taxonomic trees of bacteria built from analysis of 16S rRNA gene sequences (e.g. using RDP); there is one such object for each biological sample analyzed. Our goal is to model and formally compare a set of trees. The contribution of our work is threefold: first, a weighted tree structure to analyze RDP data is introduced; second, using a probability measure to model a set of taxonomic trees, we introduce an approximate MLE procedure for estimating model parameters and we derive LRT statistics for comparing the distributions of two metagenomic populations; and third the Jumpstart HMP data is analyzed using the proposed model providing novel insights and future directions of analysis.

Suggested Citation

  • Patricio S La Rosa & Berkley Shands & Elena Deych & Yanjiao Zhou & Erica Sodergren & George Weinstock & William D Shannon, 2012. "Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-12, November.
    • Handle: RePEc:plo:pone00:0048996
    DOI: 10.1371/journal.pone.0048996
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    References listed on IDEAS

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    2. Peter J. Turnbaugh & Ruth E. Ley & Micah Hamady & Claire M. Fraser-Liggett & Rob Knight & Jeffrey I. Gordon, 2007. "The Human Microbiome Project," Nature, Nature, vol. 449(7164), pages 804-810, October.
    3. David Banks & Kathleen Carley, 1994. "Metric inference for social networks," Journal of Classification, Springer;The Classification Society, vol. 11(1), pages 121-149, March.
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