Venn diagram of the union of the gene-probes identified by SAM.

<p>Two-class unpaired SAM analyses of ileal CD vs Control samples, UC vs. Control Samples and ileal CD vs. UC samples have been conducted. The number of gene-probes that overlapped between the three separate analyses is shown within the Venn diagram. The total numbers of upregulated and downregulated gene-probes for each individual analysis are shown on the side.</p

Selected variables associated (P≤0.05) with shifts in ileum associated microbial composition.

<p>Selected variables associated (P≤0.05) with shifts in ileum associated microbial composition.</p

Correlations between selected mRNA transcripts and bacterial genera.

<p>Selected transcripts from the Paneth cell and xenobiotic metabolism microarray clusters are listed with their public reference along the vertical axis (see text). Selected bacterial genera are classified by phyla. CD, ileal CD phenotype; Control, non-IBD control phenotype; UC, UC phenotype; F, Firmicutes; B, Bacteroidetes; P, Proteobacteria. <i>Red squares</i> represent positive correlations (P<0.05), and <i>green squares</i> represent negative correlations (P<0.05).</p

Gene list for the Paneth cell gene enriched cluster and the xenobiotic metabolism gene enriched clusters A and B.

<p>The genes selected for further correlation analyses are <b>bolded.</b></p><p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030044#pone.0030044.s003" target="_blank">Table S3</a> for the complete list of all clusters.</p