Clustering of dormancy signature scores.

<p>A) Dormancy score analysis in breast cancer cell lines. The cell lines are ordered by dormancy scores (low to high from left to right). The rows correspond to genes and the columns represent cell lines. Expression levels for positive dormancy genes (upregulated genes - top section) and negative dormancy genes (downregulated genes - bottom section) were clustered by a hierarchical clustering algorithm. The colors represent log₂ fold change compared to the average from −2.5 (blue, below average) to +2.5 (red, above average) with white as the average value. A, B, and L stand for Basal A, Basal B, and Luminal classifications, respectively. B) Correlation of cell line dormancy scores with proliferation indices from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035569#pone-0035569-t001" target="_blank">Table 1</a> of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035569#pone.0035569-Kenny1" target="_blank">[9]</a> with ER- lines plotted as squares and ER+ lines plotted as diamonds. Straight line fits of ER- (blue, Spearman correlation coefficient r = .027) and ER+ (red, r = −0.76) cell lines are plotted. The ER status of HCC1500 is unclear (ATCC indicates it as ER+ while it is ER- by gene expression and Western blot in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035569#pone.0035569-Neve1" target="_blank">[8]</a>) and it was not used in the analysis. MDA-MB-231 (large orange square), MCF7 (large green diamond) and T47D (large yellow diamond) are identified. C) Patient tumor analysis. The four clinical studies were clustered as in A. In the ER status bar, ER status is indicated by black (ER+), blue (ER−) or white (not determined) bars. The two genes for which probes were not present in the van de Vijver et al. data set are represented by gray bars. D) Comparison of clustering of cell lines and patient data. Top: Positive dormancy genes that are upregulated in high dormancy score cell lines or patients. Bottom: Negative dormancy genes that are up regulated in low dormancy score cell lines or patients.</p

Metastasis-free analysis for four clinical studies.

<p>(A, B) van de Vijver et al., (C, D) Loi et al., (E,F) Wang et al., (G, H) Pawitan et al. Kaplan Meier estimates of metastasis-free proportion among patients with high (upper third, green), medium (middle third, red), and low (bottom third, black) dormancy scores for patients with ER+ (A,C,E,F) and ER− (B,D,F,G) tumors.</p

RNAi suppression of dormancy upregulated genes accelerates tumor take and growth of ER+ luminal MCF-7 cells.

<p>(A) Percent of tumor take at the indicated time points after injecting with 4 10⁶ MCF7 cells treated with the indicated siRNAs in the mouse mammary fat pad. (B) Tumor volume (mm³) at 12 days for tumors generated by MCF7 cells treated with the indicated siRNAs and injected in the mouse mammary fat pad. (C–D) Q-PCR analysis for the expression of BHLHE41 (C) and NR2F1 (D) mRNAs after 48 hrs of treatment with control or specific siRNAs targeting these mRNAs.</p

Hazard ratios of metastasis for ER+ tumors according to dormancy score.

*<p>The metastasis-free survival times of ER + tumors in high dormancy score and low dormancy score groups were compared using Cox's proportional hazard model.</p>**<p>Hazard of metastasis among patients with low dormancy score relative to those with high dormancy score.</p>#<p>Cox's PH analysis stratified by studies using all samples from four studies.</p

Dormancy scores of ER positive and ER negative tumors.

*<p>The statistical significance of the difference in dormancy score between ER+ and ER− tumors was determined using the Mann-Whitney rank sum test.</p>#<p>Mann-Whitney rank sum test (van Elteren's test) stratified by studies using all samples from 4 studies.</p

Comparison of antibody breadth and magnitude between HIV+ and HIV- samples for the P. falciparum antigens displaying the greatest breadth of antibody reactivity in HIV+ samples.

<p>Frequency of detection in percent of samples by HIV status is reported. Significant differences in breadth are denoted by *, using Fisher exact test (two tailed, p value <0.05). Significant differences in antibody magnitude are denoted by **, and reported using the Empirical Bayes Moderated t-test, p<0.05, and an absolute log fold change > 1.</p><p>Comparison of antibody breadth and magnitude between HIV+ and HIV- samples for the P. falciparum antigens displaying the greatest breadth of antibody reactivity in HIV+ samples.</p

Hierarchical clustering of differentially abundant plasma metabolites during CM and convalescence in a paired analysis of eleven Malawian children.

<p>A heatmap of a heirarchical clustering of 247 differentially abundant (p < 0.05, FDR < 0.10, paired t test) plasma metabolites between CM and convalescence (one month later). Unsupervised hierchical clustering segregates the samples by clinical state. The asterisk notes one child with mild malaria diagnosed during the convalescent visit.</p

B cell subset analysis of HIV+ (n = 14) and HIV- (n = 21) subjects at the time of symptomatic malaria.

<p>The B cell subsets were determined by flow cytometry: naïve cells (CD19+CD10-CD21+CD27-), activated MBCs/plasmablasts (CD19+CD10-CD21-CD27+), classical MBCs (CD19+CD10-CD21+CD27+) and atypical MBCs (CD19+CD10-CD21-CD27-). The black bar denotes median values. The frequency was determined as percent of total CD19+ B cells. The Mann Whitney rank-sum test was used to compare variables between groups.</p

Breadth and magnitude of the IgG response to <i>P</i>. <i>falciparum</i> antigens by HIV status.

<p>(A) A microarray containing 824 <i>P</i>. <i>falciparum</i> proteins or protein fragments was probed with plasma samples from HIV+ (n = 18) and HIV- (n = 18) adults during symptomatic malaria. A. Venn diagrams showing the number of reactive antigens among HIV+ subjects (orange), HIV- subjects (blue), both HIV+ and HIV- subjects (purple) or neither (254). (B) Antibody breadth of HIV+ individuals (mean 83 antigens) and HIV- individuals (mean 208 antigens). Mean values and standard deviations are shown; Significant differences in breadth (Negative Binomial generalized linear model) (C) Magnitude of <i>P</i>. <i>falciparum</i> IgG responses by HIV status. We examined 384 antigens that were recognized in ≥ 10% of all samples and show the average IgG reactivity of each by HIV status. IgG reactivity is significantly higher in HIV- group (blue bars) compared to HIV+ group (orange bars) for 173 antigens. The red horizontal line indicates a p value of 0.05. (Empirical Bayes Moderated t-test, p<0.05, and an absolute log fold change > 1).</p

Associated clinical and laboratory features of Malawian children with cerebral malaria that underwent plasma metabolic profiling (n = 23).

<p>Associated clinical and laboratory features of Malawian children with cerebral malaria that underwent plasma metabolic profiling (n = 23).</p