Validation of genes up-regulated by statin in lung tissues by qPCR.

<p>Patients taking (n = 20) and not taking (n = 20) statin were matched for gender, age and smoking status. Error bars are SE on a fold-change scale. *p < 0.05, **p < 0.01.</p

Clinical characteristics of the replication cohorts according to statin treatment.

<p>NA: not available.</p><p>Clinical characteristics of the replication cohorts according to statin treatment.</p

Biological pathways of genes detected as up-regulated by statins in lung tissue.

<p>Molecules and proteins are represented by orange circles and green rectangles, respectively. Squares on lines symbolize an enzymatic reaction. Lines ending with a circle designate the activity of an enzyme. Double slashes on line indicate missing step or information. A question mark indicates a hypothetical relation. Log 2 fold changes of differentially expressed genes are indicated on the top of rectangles. (A) Genes encoding enzymes and membrane proteins involved in cholesterol synthesis that are up-regulated by statins in lung tissues. (B) (C) and (D) illustrated the possible effects of C14orf1, INSIG1 and TMEM97 on cholesterol metabolism.</p

Volcano plot of SVA analysis p-values and fold changes.

<p>Presenting the impact of statin on gene expression in the lung obtained from the discovery set. Red dots correspond to genes claimed differentially expressed (FDR < 0.05).</p

QQ-plots comparing adjustment methods.

<p>The QQ-plot is expected to follow the red line except for the extreme right (low P-values) end that may contain differentially expressed genes. A) QQ-plot of p-values obtained after linear regression of gene expression to test for genes differentially expressed between patients with and without statin therapy adjusted for age, gender and smoking status. B) QQ-plot of p-values obtained after adjusting gene expression for surrogate variables derived from SVA.</p

Clinical characteristics of the discovery cohort according to statin treatment.

<p>⁽¹⁾The type of statin was not available for one patient.</p><p>⁽²⁾Chi square test.</p><p>⁽³⁾T test.</p><p>NA: Not Available. NS: Not Significant. FEV₁: forced expiratory volume in 1 second; FVC: forced vital capacity; post-BD: post-bronchodilator. Square brackets indicate the number of missing values.</p><p>Clinical characteristics of the discovery cohort according to statin treatment.</p

Summary of top GSEA gene sets with a FDR q-value < 0.05.

<p>FDR: False Discovery Rate; FWER: FamilyWise Error Rate.</p><p>Gene sets from canonical pathway databases are shown in bold.</p><p>Summary of top GSEA gene sets with a FDR q-value < 0.05.</p

Genes (probe sets) differentially expressed between statin groups in the discovery and replication cohorts.

<p>CI is the confidence interval: the value to add and subtract to the log 2 fold change (Log2FC). BH is the Benjamini-Hochberg adjusted p-values. Genes in bold are replicated in at least one cohort (Groningen). Some genes are represented by more than one transcript.</p><p>Genes (probe sets) differentially expressed between statin groups in the discovery and replication cohorts.</p

Additional file 1: of Gene expression analysis in asthma using a targeted multiplex array

Supplementary Methods – Methods describing selection of house keeping genes and immunohistochemical staining procedure. Supplementary Tables – Tables containing clinical demographics for subjects, average counts, fold change, and p-value for all genes studied, and all differentially co-expressed genes. Supplementary Figures and Legends – Figures showing sample immunohistochemical staining for proteins of significantly altered genes, co-expression plots. (DOCX 35 kb

Volcano plot of gene differentially expressed between statin users and non-users.

<p>The plot shows the log fold-change on the X-axis versus the unadjusted P values (on the–log10 scale) on the Y-axis. The blue and red dots represent genes that showed fold change in either direction that is greater than 0.05 and have unadjusted P value <0.01. Genes that had an FDR-adjusted P value less than 0.05 for differential expression are annotated on the graph.</p