Best features to discriminate by activity levels.

<p>Activity levels are considered simultaneously, employing the Kruskal-Wallis test. Grey bar indicate the q-value and thus the strength of the association between the features and the disease state. Color bars indicate the average percentage of reads for each disease activity level.</p

demographics of paediatric (training) cohort.

<p>demographics of paediatric (training) cohort.</p

Stratification of patients by activity levels.

<p>Overall microbial diversity as measured by the Shannon Diversity Index. Activity was assessed on the basis of patient symptoms using PCDAI and PUCAI clinical indices.</p

Taxa significantly associated with IBD.

<p>Center panel is a compositional heatmap of the selected taxa for each of the samples in the pediatric case-control study. Left panel indicates the significance of the association of each taxa with disease state, as measured by the q-value. Right panel shows a measure of effect size (Cohen’s delta), highlighting in red those taxa which are significantly more prevalent in IBD samples. Bottom panels show relevant metadata for each sample, including disease activity as measured by PUCAI <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039242#pone.0039242-Tomas1" target="_blank">[32]</a> and PCDAI indices <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039242#pone.0039242-Knights1" target="_blank">[33]</a>.</p

Accuracy of disease classification.

<p>(A) SLiME applied to Frank et al. biopsy data set. The black line indicates performance obtained when features were generated by taxonomical binning of the original sequence data (AUC  = 0.73); dashed line shows performance when features were selected based on their importance in the pediatric case-control data set and then applied to the Frank et al. study (AUC  = 0.71). (B) ROC curve for SLiME classification of active IBD patients vs controls in the pediatric case-control data set. Two different threshold selections are highlighted: circle, for which SLiME has 80.3% sensitivity and 69.7% specificity; triangle, for which SLiME has 45.8% sensitivity and 92.4% specificity.</p