Additional file 1. of Antimicrobial activity of customary medicinal plants of the Yaegl Aboriginal community of northern New South Wales, Australia: a preliminary study

Picture showing typical results of the disc diffusion assay

Clinical characteristics of patients in stem-like and differentiated subtypes.

**<p>p-value <0.01,</p>***<p>p-value <0.001. OSE Ovarian surface epithelium, NC not classified. In each dataset, p-values were corrected for family-wise error rate using Hommel’s method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057799#pone.0057799-Hommel1" target="_blank">[46]</a>, except for the test for association with the Tothill et al. molecular subtypes.</p

Shared characteristics of Types I and II ovarian cancer and the stem-like and differentiated subtypes [12].

<p>Shared characteristics of Types I and II ovarian cancer and the stem-like and differentiated subtypes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057799#pone.0057799-Kurman1" target="_blank">[12]</a>.</p

Multivariate Cox proportional hazards models of the stemness bipartition to predict relapse-free survival when adjusting for two prognostic variables (A) residual disease and stage, (B) grade and stage or (C) grade and residual disease.

*<p>p<0.05,</p>**<p>p<0.01,</p>***<p>p<0.001.</p>1<p>In regression analyses, the ordinal variables stage and grade were broken into multiple components using default functions in R. However, only the linear components (levels treated as a continuous variable) are displayed in the table because the other components were not significant. Grade was also coded as a quadratic component (grade 2 vs. grades 1 and 3) and stage as both quadratic (stages 2 and 3 vs. stages 1 and 4) and cubic (stage 2> stage 4> stage 1> stage 3) components.</p

The stem-like subtype is significantly overrepresented in basal-like breast cancer.

***<p>Fisher’s exact test p = 3.50×10⁻¹⁸ and p = 1.11×10⁻²⁷, Desmedt and Veridex datasets respectively.</p

The PLASQ Procedure for Determining ASCN and PSCN from the .cel Files

<p>After normalizing signal intensities from all samples, the model is first fit to the normal samples' data to produce both genotype calls and parameter estimates at each SNP site. The latter are used in the model as applied to the data from the cancer samples. Ordinary least squares fitting produces raw ASCN estimates at each SNP. The corresponding raw total copy number estimates are smoothed using circular binary segmentation. Finally, further processing yields our final ASCN and PSCN inferences (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010065#s4" target="_blank">Materials and Methods</a>). EM algorithm, expectation-maximization algorithm.</p

Average Intensities for Each Probe Type by Sample at a Single SNP (rs 2273762)

<p>The inset table gives the average background-subtracted intensities that would be predicted by our model. The actual background-subtracted mean intensity values (bar graph) in each sample closely agree with what is predicted (inset table).</p

Heatmap of gene expression and Kaplan-Meier survival curves for the stemness bipartition.

<p>(A) A heatmap of gene expression profiles of the 24 differentiated (green) and 121 stem-like (blue) tumors from the AOCS dataset <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057799#pone.0057799-Tothill1" target="_blank">[10]</a>. The tumors are ordered by increasing stemness molecular subtype score, and the 51 classifier genes are ordered from top to bottom by increasing over-expression in the stem-like subtype according to a pooled <i>t</i>-test. The Kaplan-Meier curves are with respect to (B) disease-free survival and (C) overall survival and are not significant at p<0.05, but this is possibly due to the small size of the differentiated subtype.</p

Validation of the stemness bipartition in independent ovarian cancer microarray datasets, as well as in the remaining AOCS dataset.

<p>In the remaining AOCS dataset, the stem-like subtype has strongly worse (A) disease-free survival (p<0.001) and (B) overall survival (p = 0.00127). In the (C) Crijns and (D) Dressman datasets, the stem-like subtype has significantly worse overall survival (p = 0.022 and p = 0.035, respectively).</p