Additional file 1.

Figure S1. Overview of the analysis pipeline. (a) Stool samples were obtained from six breast-fed and six formula-fed infants. (b) Gut microbial DNA and host gut-epithelial mRNA were isolated and sequenced/hybridized. (c) Microbial DNA sequence was analyzed for functional content and taxa using MG-RAST and PhymmBL; gut epithelial mRNA was analyzed for eukaryotic gene function using microarray. (d) Significant multivariate correlations between gut-epithelium mRNA expression and metagenomic DNA frequency were determined using multivariate canonical correlation analysis (CCA) repeated on subsets of host gene expression data.

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Schwartz et al. Genome Biology 2012 13:r32   doi:10.1186/gb-2012-13-4-r32