Additional file 8: Table S7. of Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks

Significantly enriched pathways of early and late responding genes after irradiation with 8 Gy. Pathways with FDR < 0.1 were considered statistically significant. (XLSX 102 kb

Additional file 5: Table S4. of Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks

Technical validation of microarray data. Eight of the differentially expressed genes detected with the microarray technology were arbitrarily chosen for technical validation by qRT-PCR. Correlation analysis results (Spearman’s rho coefficient) and fold-changes (microarray and qRT-PCR) are shown. Asterisks (*) indicate fold-change values for genes detected as differentially expressed by microarray analysis. (DOCX 52 kb

Additional file 12: of Integrative analysis of the microRNA-mRNA response to radiochemotherapy in primary head and neck squamous cell carcinoma cells

Primer sequences for TP53 and EGFR sequencing. (PDF 42 kb

Additional file 7: of Integrative analysis of the microRNA-mRNA response to radiochemotherapy in primary head and neck squamous cell carcinoma cells

Significantly deregulated mRNAs in primary HN2092 after in vitro radiochemotherapy treatment. (PDF 143 kb

Additional file 8: of Integrative analysis of the microRNA-mRNA response to radiochemotherapy in primary head and neck squamous cell carcinoma cells

Pathway enrichment analysis of differentially expressed genes in HN1957 after radiochemotherapy treatment. (PDF 66 kb

Example of fitted spline regression models.

<p>The plot shows spline regression models fitted to the measured time-course expression data of an arbitrary chosen gene (BBC3). The blue line represents the fitted model for the control (0 Gy) and read line that for the irradiated group (1 Gy). Blue and red dots represent the measured expression levels of the biological replicates. Vertical lines represent the endpoints and interior knots correspond to the 0.33- and 0.66-quantiles.</p

Comparison of NCSRM and BETR methods with respect to the top 10 pathways after mapping of 5% highest ranked genes from the reconstructed gene association networks.

Comparison of NCSRM and BETR methods with respect to the top 10 pathways after mapping of 5% highest ranked genes from the reconstructed gene association networks.</p

Number of genes subjected to GAN reconstruction and properties of resulted GANs.

<p>Number of genes subjected to GAN reconstruction and properties of resulted GANs.</p

Comparison of hub genes in networks resulting from different methods.

<p>Comparison of hub genes in networks resulting from different methods.</p

Schematic workflow of the analysis of gene expression time-course data.

<p>Samples were collected 0.25, 0.5, 1, 2, 4, 8 and 24 hours after sham or actual irradiation. Transcriptional profiling was performed using Agilent gene expression microarrays and comprises three major steps: the identification of differentially expressed genes from time-course expression data by employing a natural cubic spline regression model; the use of regularized dynamic partial correlation method to infer gene associations networks from differentially expressed genes and the topological identification and functional characterization of the key nodes in the reconstructed networks.</p