Figure 5

Boxplots of the distributions of all the gene pair relative expression levels calculated across all cell lines for the different platforms. From a total number of 4,851 possible gene pair combinations based on the array measurements of 12 out of the 14 genes (excluding ERBB2 and RPS6KB1 and data points (RAG2 and CASP5) not available from QRT-PCR) in the 3 cell lines (3 replicate arrays each) a total number of 3,321 and 3,828 combinations were considered for ratio and single intensity array data, respectively. See [Additional file 4] for the number of possible versus available gene pair combinations for the QRT-PCR and array data, respectively. Combinations were then attributed to one of 9 different fold-change bins based on the -ΔΔCt (for A – C) or -ΔCt (D and E) values calculated from the QRT-PCR data with the following code (in bold) corresponding the following geneA/geneB log₂-ratios (x) intervals: < -5: x < -5; -3: -5 = x < -1.25; -1: -1.25 = x < -0.75; -0.5: -0.75 = x < -0.25; 0: -0.25 = x < 0.25; 0.5: 0.25 = x > 1.25; 1: 0.25 = x > 1.25; 3: 1.25 = x > 5.0; > = 5: x = 5.0. For each gene pair combination we assessed the corresponding FCs either from the (1) array log₂-ratio (cell line/REF) data (Affymetrix, Amersham, and Agilent, shown in A – C, respectively) or from (2) log₂-intensities (Affymetrix and Amersham data only, shown in D and E).