- Selected oral presentation
- Open Access
Statistical methods for comparing the abundances of metabolic pathways in metagenomics
https://doi.org/10.1186/gb-2010-11-s1-o7
© Liu and Pop; licensee BioMed Central Ltd. 2010
- Published: 11 October 2010
Keywords
- Homocysteine
- Obese Subject
- Metabolic Network
- Homocysteine Level
- Energy Harvest
Background
A major goal of metagenomic studies is to identify specific functional adaptations of microbial communities to their habitats. The functional profile and the abundances for a sample can be estimated by mapping metagenomic sequences to the global metabolic network consisting of thousands of molecular reactions. Here we describe our development of statistical methods that can identify differentially abundant subnetworks between metagenomic samples.
Methods
First, we introduced a scoring function for an arbitrary subnetwork and find the max-weight subnetwork in the global network by greedy search. Then we compute p abund and p struct values using nonparametric approaches to answer two statistical questions: (i) Is this sub-network differentially abundant? (ii) What is the probability of finding such good subnetworks by chance? Significant metabolic subnetworks are detected on the basis of these two p values.
Results
Performance on simulated datasets. Our methods MetaPath outperforms Anneal and Greedy (Ideker et al, 2002), KEGGPath and Metastats (White et al, 2009) on four simulated datasets. n is the number of reactions in the subnetwork and p is their significance.
Homocysteine pathways are enriched in (a) obese and (b) infant subjects.
Conclusions
We have developed statistical methods to find differentially abundant metabolic pathways in metagenomics. The performance is better than previous approaches. Results from real metagenomic datasets confirm previous observations and also provide several new biological insights.
Authors’ Affiliations
References
- Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI: An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006, 444: 1027-1031. 10.1038/nature05414.PubMedView ArticleGoogle Scholar
Copyright
This article is published under license to BioMed Central Ltd.