Graphical representation of the ISOpure-S1 algorithm.

<p>The ISOpure-S1 algorithm is based on a probabilistic topic model. We modeled post-treatment gene expression profiles as mixtures of hidden profiles corresponding to treatment-response and treatment-naive portions, and removed the gene expression signals of the treatment-naive portion using pre-treatment expression profiles. (A) We modeled the post-treatment expression profile as a weighted average of the gene expression profiles of treatment-response and treatment-naive profiles. (B) We inferred a single common treatment-response profile after drug treatment across all patients that corresponds to the portion of the post-treatment profiles that cannot be attributed to any pre-treatment profiles. (C) We used this inferred treatment-response profile to estimate the % treatment-response content in each patient. Steps (B) and (C) were done iteratively during the maximum likelihood estimation procedure.</p

The per-patient % treatment-response estimates made by ISOpure-S1, sorted by increasing order (green dots).

<p>A sensitivity analysis was performed to verify the robustness of our results (blue dots), which was done by dividing the total set of profiled genes into four subsets and applying ISOpure-S1 on each subset separately. The % treatment-response estimates for each subset of the profile (blue dots) are similar to the original results (green dots) (average standard error = 0.019; maximum standard error = 0.057).</p

A decrease in the proportion of T-cells, neutrophils, monocytes and platelets in blood may be associated with a response to drug treatment.

<p>We correlated the delta profile with the profiles of 38 known blood cell types. The red color indicates a decrease in their concentrations and the blue color indicates an increase in their concentrations in blood in response to drug treatment. The color bar indicates the Spearman correlation coefficients.</p

Correlation between ISOpure-S1-predicted % treatment-response and % decrease in clinical indicators of disease activity.

<p>Correlation between ISOpure-S1-predicted % treatment-response and % decrease in clinical indicators of disease activity.</p

Correlation between expression-based % treatment-response estimate inferred by ISOpure-S1 and % reduction in number of active joints found in clinical record.

<p>Left: Correlation between % treatment-response estimate and % reduction in number of active joints (Pearson rho = 0.44, p = 0.010; Spearman rho = 0.46, p = 0.008). Right: The patients were divided evenly into three groups based on their % treatment-response estimates. The median and interquantile range of % reduction in number of active joints are indicated by box plots.</p

PERT recovers compositions of uncultured human cord blood mono-nucleated and lineage-depleted (Lin-) cells.

<p>(A) Schematic compositions of mono-nucleated cell samples and Lin- cell samples. (B) Model predicted proportions of 11 homogeneous blood cell lineages, namely granulocytes (GRAN), erythrocytes (ERY), monocytes (MONO), precursor B cells (PREB), megakaryocyte-erythrocyte progenitors (MEP), megakaryocytes (MEGA), primitive progenitor cells (PPC), eosinophils (EOS), granulocyte-monocyte progenitors (GMP), common myeloid progenitors (CMP), and basophils (BASO) in uncultured human mono-nucleated cord blood cell samples. (C) Flow cytometry measured proportions of the 11 blood cell lineages in the uncultured human mono-nucleated cord blood cell samples shown in (B). (D) Model predicted proportions in uncultured human Lin- cord blood cell samples. (E) Flow cytometry measured proportions in the uncultured human Lin- cord blood cell samples shown in (D). (F) R² calculated from the Pearson's correlation coefficients between the model predicted cell proportions and the ones assigned by flow cytometry. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002838#pcbi-1002838-t002" target="_blank">Table 2</a> for the associated t-statistics and P-values. (G) Averaged absolute differences of model predicted cell proportions. Error bars show standard deviations of the absolute differences between model predicted and flow cytometry assigned proportions of the 11 blood cell lineages. (H) The Bayesian information criterion (BIC) calculated from the parameters in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002838#pcbi-1002838-t001" target="_blank">Table 1</a>.</p

ISOpure-S1-inferred compositions of post-treatment profiles in terms of pre-treatment profiles and “treatment-response” profile.

<p>Each post-treatment profile was attributed to a combination of the pre-treatment profiles (column 1–29) and the “treatment-response” profile (column 30). The shading represents the percentage contribution from each of the pre-treatment profiles and the “treatment-response” profile.</p

Measures of disease activity in patient cohort.

<p>Measures of disease activity in patient cohort.</p