Receiver operating characteristic (ROC) curve for different classification methods on the training set.

<p>Receiver operating characteristic (ROC) curve for different classification methods on the training set.</p

Classification results on the training and test sets.

<p>The accuracy, sensitivity, specificity of the ileal gene signature selected by the boosting method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037139#pone.0037139-Smyth2" target="_blank">[16]</a> are calculated using Leaving-One-Out cross validation on the training and subsequently, direct classification of the test set based on the training set.</p

Comparison of 17 ileal gene signatures selected by four different feature selection methods.

<p>Boosting <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037139#pone.0037139-Smyth2" target="_blank">[16]</a>, PAM) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037139#pone.0037139-Tusher1" target="_blank">[17]</a>, random forest <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037139#pone.0037139-Bhlmann1" target="_blank">[18]</a> and LASSO <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037139#pone.0037139-Tibshirani1" target="_blank">[19]</a> were applied to the SAM filtered training microarray dataset to select 17 ileal gene signatures. The AUC and overall accuracy for each of the signatures were calculated based on the majority vote of 7 classifiers (Boosting, PAM, Random Forest, LASSO, Support Vector Machine, Linear Discriminant Analysis, and Naive Bayes), which is equivalently to the decision based on the median score using an usual probability threshold of 0.5 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037139#s2" target="_blank">Materials and Methods</a>).</p

Patient characteristics associated with each disease phenotype in the training and test sets.

<p>Patient characteristics associated with each disease phenotype in the training and test sets.</p

Immunohistochemical localization of FOLH1 in disease unaffected ileal mucosa from the proximal margin of resected ileum from an ileal CD subject (left panel) and a control non-IBD subject.

<p>The more prominent FOLH1 staining in the ileal CD sample is localized to the villous epithelium. Magnification is 100×. Bar is 200 µm.</p

Receiver operating characteristic (ROC) curve for different classification methods on the test set.

<p>Receiver operating characteristic (ROC) curve for different classification methods on the test set.</p

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

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

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

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