Average number of A,C,G,T and occurrence of two or more consecutive Gs in probe sequence for the 10 most and the 10 least affected genes and p values for all affected compared to remaining genes.

a<p>Mann-Whitney U test.</p

Flowchart illustrating experimental procedure.

<p>Description of the procedures used to assess samples from RNA extraction to acquiring of gene lists, including samples removed following each step of analysis. Tumour samples are abbreviated T and controls C.</p

Linear regression analysis.

<p>Regression model describing how much of the variation in sample quality (Ct_diff) can be explained by sample storage time prior to extraction.</p

Confirmation of four genes in 20 fresh frozen sample using qPCR.

a<p>Wilcoxon matched pairs signed rank test.</p

Example of three genes and how their expression was affected by difference in sample quality (Ct_diff).

<p>(A), (B) and (C) Linear regression analysis of the genes YPEL5, TRPM4 and the short non-coding gene SNORA10 describing the relationship between expression of the gene and sample quality (CT_diff). All 78 samples are included and analysis was performed using non-normalized data. (D), (E) and (F) Linear regression analysis of the same genes using normalized data. Samples and regression line for tumours are denoted in blue and sample and regression line for controls in red.</p

Linear regression analysis.

<p>Regression model describing how much of the variation in number of detected genes on the array can be explained by sample quality after extraction (Ct_diff).</p

Pathway analysis of significant genes.

<p>Pathway analysis of significant genes.</p

Quality measurements of FFPE controls and tumours.

a<p>Mann-Whitney U test.</p>b<p>4 samples did not generate sufficient RNA (<40 ong).</p>c<p>1 sample failed the PCR reaction.</p>d<p>4 tumours and 1 control failed to fulfil array requirements.</p

Dendogram from unsupervised hierarchical clustering.

<p>Including the 43 samples selected for differential gene expression analysis and all 12579 genes detected in these samples. Control samples are denoted by C and tumours by T. Pearson correlation was used as a measurement of similarity.</p

Additional file 3: of ΔNp63α expression induces loss of cell adhesion in triple-negative breast cancer cells

List of genes whose expression was changed 24 h after induction of ∆Np63α or TAp63α expression in MDA-MB-468 cells. (PDF 503 kb