Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)
| Autor: | Stéphane Dray, D. Aguirre de Cárcer, Sandrine Pavoine |
|---|---|
| Přispěvatelé: | Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS) |
| Rok vydání: | 2014 |
| Předmět: |
16S
Multivariate statistics [SDV]Life Sciences [q-bio] Statistics as Topic 18S Biology computer.software_genre DNA Ribosomal DPCoA RNA Ribosomal 16S Genetics microbial community analysis Phylogeny Ecology Evolution Behavior and Systematics External variable Phylogenetic tree Ecology QIIME Unifrac Principal (computer security) Sequence Analysis DNA Biota UniFrac Distance matrix A priori and a posteriori Ordination Data mining computer Biotechnology |
| Zdroj: | Molecular Ecology Resources Molecular Ecology Resources, 2015, 15 (2), pp.242-9. ⟨10.1111/1755-0998.12300⟩ Digital.CSIC. Repositorio Institucional del CSIC instname Molecular ecology resources Molecular ecology resources, 2015, 15, pp.242-9 |
| ISSN: | 1755-098X 1755-0998 |
| Popis: | © 2014 John Wiley & Sons Ltd. The use of next-generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and (or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene data sets. |
| Databáze: | OpenAIRE |
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