Fig. 2
Circulating tumor cells (CTCs) undergo massive transcriptional reprogramming and possess a distinct gene expression profile (GEP). A Heat map representation of pair-wise correlations of normalized expression data from (left) GEP1 and (right) GEP2 experiments in MDA-MB-231 xenografts (“a”, axillary; “i”, inguinal; “(c)”, controlateral to PT; “(h)”, homolateral to PT; “(d)”, distal section; “(p)”, proximal section). B Heat map representation of the expression pattern of the most variable genes (interquartile range intensities >95th percentile) in (left) GEP1 and (right) GEP2. C Bar chart of the experimental variability according to principal variance component analysis in (left) GEP1 and (right) GEP2. D Scatter plot of correlations among log2(fold changes) considering all detected genes (dots) in GEP1 and GEP2, in pair-wise sample class comparisons. Genes significantly up-regulated or down-regulated (fold change threshold=│2│and false discovery rate <0.05) in both experiments are represented by red and green dots, respectively, and genes with discordant trend are represented by pink or blue dots if up-regulated in GEP1 AND down-regulated in GEP2 or down-regulated in GEP1 AND up-regulated in GEP2, respectively. E Network representation of Gene Ontology (GO) terms enriched in the lists of genes significantly (left) up-regulated or (right) down-regulated in the comparison between CTCs and solid lesions using GEP1 and GEP2 data. Nodes represent significantly enriched GO terms, size and color are proportional to the number of genes annotated in the term and to their significance (darker color, higher statistical significance), respectively. Nodes that share common genes are connected by an edge, with thickness proportional to the overlap coefficient (OC) between the two terms, calculated as |A∩B|/min(|A|, |B|). Only terms with an OC≥0.5 are shown. F Plot of the mean±standard deviation relative expression (ΔCq, normalized equivalent threshold cycle) of a panel of MDA-MB-231-CTC up-regulated genes and of CD45 gene (PTPRC) in the CTC fraction and tumor biopsy of n=4 patients