Infliximab concentration (A), Highly Sensitive [HS]–CRP (B) and Fecal Calprotectin (C) during infliximab therapy.

<p>Empty long dash lines: control patients (treated with infliximab 5 mg/Kg); Filled lines: study subjects (treated with infliximab 3 mg/Kg). Square dot lines indicate the upper limit of the normal range for HS-CRP and Fecal Calprotectin. Values are reported as mean and standard error (vertical bars). The asterisk denotes a significant difference (p < 0.05) between controls and study subjects at a given time point during the 8-week therapeutic interval.</p

Study Design.

<p>Patients subjected to prophylactic infliximab [IFX] 5 mg/Kg after surgery and in full remission after 3 years of therapy showed endoscopic recurrence in 83% of cases when the medication was stopped. Those with recurrence (n = 10) re-started IFX in a dose optimization study in which we showed that 3 mg/Kg were sufficient to re-induce and maintain endoscopic remission for 1 year in all patients (ref.2). Five of these ten patients participated in the current study. Antibodies To Infliximab [ATI] and Infliximab Trough Levels [ITL] were measured and compared to those of CD patients who did not undergo surgery in remission on a standard 5 mg/Kg IFX dose. After an additional 18 months the patients treated with 3 mg/Kg IFX underwent colonoscopy.</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

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

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

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