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Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data
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 H...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494672/ https://www.ncbi.nlm.nih.gov/pubmed/23152838 http://dx.doi.org/10.1371/journal.pone.0048996 |
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author | La Rosa, Patricio S. Shands, Berkley Deych, Elena Zhou, Yanjiao Sodergren, Erica Weinstock, George Shannon, William D. |
author_facet | La Rosa, Patricio S. Shands, Berkley Deych, Elena Zhou, Yanjiao Sodergren, Erica Weinstock, George Shannon, William D. |
author_sort | La Rosa, Patricio S. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3494672 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-34946722012-11-14 Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data La Rosa, Patricio S. Shands, Berkley Deych, Elena Zhou, Yanjiao Sodergren, Erica Weinstock, George Shannon, William D. PLoS One Research Article 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. Public Library of Science 2012-11-09 /pmc/articles/PMC3494672/ /pubmed/23152838 http://dx.doi.org/10.1371/journal.pone.0048996 Text en © 2012 La Rosa et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article La Rosa, Patricio S. Shands, Berkley Deych, Elena Zhou, Yanjiao Sodergren, Erica Weinstock, George Shannon, William D. Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data |
title | Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data |
title_full | Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data |
title_fullStr | Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data |
title_full_unstemmed | Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data |
title_short | Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data |
title_sort | statistical object data analysis of taxonomic trees from human microbiome data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494672/ https://www.ncbi.nlm.nih.gov/pubmed/23152838 http://dx.doi.org/10.1371/journal.pone.0048996 |
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