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Genome Biol DOI:10.1186/gb-2011-12-6-r60

Metagenomic biomarker discovery and explanation.

Publication TypeJournal Article
Year of Publication2011
AuthorsSegata, N, Izard, J, Waldron, L, Gevers, D, Miropolsky, L, Garrett, WS, Huttenhower, C
JournalGenome Biol
Volume12
Issue6
PagesR60
Date Published2011 Jun 24
ISSN1474-760X
KeywordsAdult, Animals, Bacteria, Biomarkers, Colitis, Ulcerative, Data Mining, Humans, Infant, Metagenome, Metagenomics, Mice, Mice, Inbred BALB C, Mice, Knockout, Mucous Membrane, Sensitivity and Specificity, Software, Viruses
Abstract

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

URLhttp://genomebiology.com/content/12/6/R60
DOI10.1186/gb-2011-12-6-r60
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/21702898?dopt=Abstract

Alternate JournalGenome Biol.
PubMed ID21702898
PubMed Central IDPMC3218848
Grant ListAI078942 / AI / NIAID NIH HHS / United States
K08 AI078942 / AI / NIAID NIH HHS / United States
R01 CA154426 / CA / NCI NIH HHS / United States
R21 DE017106-02 / DE / NIDCR NIH HHS / United States
1R01HG005969 / HG / NHGRI NIH HHS / United States
R01 HG005969 / HG / NHGRI NIH HHS / United States
R21 DE017106 / DE / NIDCR NIH HHS / United States
DE017106 / DE / NIDCR NIH HHS / United States