Top 50 genes differentially up regulated in theca interna from small follicles.

<p>The fold change is the ratio of signal intensity of theca interna to granulosa cells from microarray analyses.</p><p>*Genes in bold are common to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119800#pone.0119800.t005" target="_blank">Table 5</a>.</p><p>Top 50 genes differentially up regulated in theca interna from small follicles.</p

Number of probe sets and genes differentially expressed in large healthy follicles with respect to small follicles.

<p>Statistical difference with <i>P</i><0.05 was determined by ANOVA using the step up Benjamini-Hochberg False Discovery Rate method for multiple corrections in Partek Genomics Suite Software.</p

Expression data for up regulated genes in thecal layers from small and large follicles.

<p>The data are shown as the mean ± SEM (n = 10 for small follicle group, n = 5 for large follicle group, GC = granulosa cells, TI = theca interna). qRT-PCR values were determined from the geometric mean of 2^-ΔΔCt of the target genes to the cyclophilin A (<i>PPIA</i>) and glyceraldehyde phosphate dehydrogenase (<i>GAPDH</i>), and the microarray values are signal intensities (normalized but not log transformed). Significantly different results for qRT-PCR were determined by one-way ANOVA with Tukey’s post hoc test. The <i>P</i> values for the microarray results were corrected for multiple testing using the FDR. All values which are statistically different from each other are indicated by different alphabetical symbols in the graphs.</p

Genes down-regulated in atretic compared with healthy follicles.

<p>≥2 fold-change with <i>P</i><0.05 by Benjamini-Hochberg post-hoc test for multiple corrections following one-way ANOVA and categorized by function. Assignation of genes to categories was determined manually by the authors based on available information from NCBI databases and literature. Genes are listed in descending order of fold change within each category.</p

Primer sequences used for qRT-PCR.

<p>Primer sequences used for qRT-PCR.</p

Unsupervised PCA of arrays from theca interna of small healthy and atretic follicles.

<p>The healthy follicles were separated into rounded (n = 5) and columnar (The graph is a scatter plot of the values for the first (X-axis) and second (Y-axis) principal components based on the Pearson correlation matrix of the total normalized array intensity data. The numbering of each sample enables the samples in this figure to be identified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099706#pone.0099706.s001" target="_blank">Fig. S1</a>. Abbreviations are: thecal sample healthy rounded (TSHR), thecal sample healthy columnar (TSHC) and thecal sample atretic (TSA).</p

Measurement of gene expression by qRT-PCR.

<p>The data are shown as the mean ± SEM (n = 7 for small follicle group, n = 4 for large follicle group). qRT-PCR values were determined from the mean of the ratio of 2^−ΔCt of the target genes to cyclophilin A (<i>PPIA</i>) and glyceraldehyde phosphate dehydrogenase (GAPDH), and the microarray values are signal intensities (normalized but not log transformed). Significantly different results for qRT-PCR were determined by Student's <i>t</i>-test. The <i>P</i> values for the microarray results are corrected for multiple testing using the FDR (*<i>P</i><0.05, **<i>P</i><0.01 and ***<i>P</i><0.001).</p

A list of 4 upstream regulators predicted to be activated or inhibited in IPA.

†<p>The predicted activation state is inferred from the bias-corrected z-score.</p>††<p>The bias-corrected z-score is computed based on the proportion of target genes present in the data set which are directionally regulated as expected according to known effects of the regulator on the target compiled from the literature.</p><p>**The <i>P</i> value of overlap measures the statistical significance of overlap using Fisher's exact <i>t</i>-test, between genes from the data set and those known to be acted upon by an upstream regulator.</p

The top six upstream regulators predicted by IPA to be activated in atretic versus healthy follicles.

†<p>The predicted activation state is inferred from the bias-corrected z-score. The bias-corrected z-score is computed based on the proportion of target genes present in the data set which are directionally regulated as expected according to known effects of the regulator on the target compiled from the literature.</p><p>*The <i>P</i> value of overlap measures the statistical significance of overlap using Fisher's exact <i>t</i>-test, between genes from the data set and those known to be acted upon by an upstream regulator.</p

Number of probe sets and genes differentially expressed in atretic compared with healthy follicles.

<p>Determined by ANOVA with <i>P</i><0.05 by the step-up Benjamini Hochberg FDR method for multiple corrections using Partek Genomics Suite Software.</p