Correlation of gene expression profiles.

<p>A) <b>The same cell types</b>: Left panels: a near-unity Pearson correlation, <i>r</i>, in whole gene expression (<i>N</i>: total number of mRNAs) within the same cell type is shown for different types of molecular stimulation (first row: HRG- vs. EGF-stimulated MCF-7 cells; second row: DMSO- vs. atRA-stimulated HL-60 cells). Right panels: 313 (<i>n</i>) gene expressions, which have a common probe ID among four transcriptome microarray expression data sets (see <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167912#sec005" target="_blank">Methods</a></b>) also show a near-unity Pearson correlation within the same cell type. B) <b>Different cell types (</b><i>n</i> = 313 gene expressions): The near-unity Pearson correlation between independent samples of the same cell type breaks down when the gene expression profiles come from different (HL-60 and MCF-7) cell types. <i>ε</i>(<i>t</i>) represents the ensemble of expression at time point <i>t</i> (<i>N</i>: the whole set; <i>n</i>: an ensemble set) and <i>ln</i>(<i>ε</i>(<i>t</i>)) represents its natural logarithm, where the natural log of an individual expression value is taken. Plots show <i>t =</i> 90min for MCF-7-stimulated cells and <i>t =</i> 18h for HL-60-stimulated cells.