Additional file 3: Figure S2. of uPAR enhances malignant potential of triple-negative breast cancer by directly interacting with uPA and IGF1R

Combined RNAi of uPAR and IGF1R significantly reduced the tumourigenic potential of TNBC cells. a: Representative Western blot analysis of uPAR and IGF1R following RNAi using three different siRNAs per target protein, respectively and of (b) MMP2 and MMP9. Tubulin was used as loading control. c: In vitro viability assays (n = 5), d: scratch wound assays (n = 3) and (e) matrigel invasion assays (n = 3) are shown 48 h post-transfection. siRNAs for transient downregulations of target proteins or of GAPDH (positive control) and a non-targeting siRNA as negative control were used in triplicates according to previous protocol [37]. f: Relative mRNA levels of uPAR, IGF1R and uPA following stable RNAi of target proteins determined by qRT-PCR (n = 3) are shown. The quantifications were determined in relation to mock control. Standard deviations and p-values are shown. (PDF 336 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

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 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

Comparison of hub genes in networks resulting from different methods.

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

Additional file 2: Figure S1. of uPAR enhances malignant potential of triple-negative breast cancer by directly interacting with uPA and IGF1R

Combined RNAi of uPAR and uPA significantly reduced the tumourigenic potential of TNBC cells. a: Representative Western blot analysis of uPAR and uPA following RNAi using three different siRNAs per target protein, respectively and of (b) MMP2 and 9, (phospho) STAT3, Paxillin. Tubulin was used as loading control. c: In vitro viability assays (n = 5), d: scratch wound assays (n = 3) and (e) matrigel invasion assays (n = 3) are shown 48 h post-transfection. siRNAs for transient downregulations of target proteins or of GAPDH (positive control) and a non-targeting siRNA as negative control were used in triplicates according to previous protocol [37]. The quantifications were determined in relation to mock. Standard deviations and p-values are shown. (PDF 329 kb

Number of detected and differentially expressed genes for each dose and cell lines for NCSRM and BETR methods.

<p>Number of detected and differentially expressed genes for each dose and cell lines for NCSRM and BETR 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

Additional file 1: Table S1. of uPAR enhances malignant potential of triple-negative breast cancer by directly interacting with uPA and IGF1R

Overview of applied primary antibodies for immunohistochemical analyses (IHC) and Western blots (WB). (DOC 53 kb

Additional file 2: Figure S1. of uPAR enhances malignant potential of triple-negative breast cancer by directly interacting with uPA and IGF1R

Combined RNAi of uPAR and uPA significantly reduced the tumourigenic potential of TNBC cells. a: Representative Western blot analysis of uPAR and uPA following RNAi using three different siRNAs per target protein, respectively and of (b) MMP2 and 9, (phospho) STAT3, Paxillin. Tubulin was used as loading control. c: In vitro viability assays (n = 5), d: scratch wound assays (n = 3) and (e) matrigel invasion assays (n = 3) are shown 48 h post-transfection. siRNAs for transient downregulations of target proteins or of GAPDH (positive control) and a non-targeting siRNA as negative control were used in triplicates according to previous protocol [37]. The quantifications were determined in relation to mock. Standard deviations and p-values are shown. (PDF 329 kb