Additional file 9.

Figure S5 - Magnitude of immune metagene expression correlates with abundance of immune cell infiltrate. Histological characterization of immune cell abundance was previously conducted for 35 tumors (22 ER+, 13 ER-) from Guy's Hospital, London [29], for which corresponding tumor material was profiled on expression microarrays and included in our multi-study microarray database [97]. (A) Distributions of mean-centered metagene values (977A) are shown as box and whisker plots for each measure of immune cell abundance (L = low, I = intermediate, H = high). Shaded rectangles define the interquartile ranges. The midline of each rectangle marks the median value. T-bars extending from the interquartile range mark the 5th and 95th percentiles, and outliers are indicated by open circles. P-values for differential distributions were generated by Kruskal-Wallis one-way analysis of variance by ranks (Sigma Plot 11.0). (B-D) Genes representative of the T/NK and B/P metagenes were prospectively analyzed for expression in a panel of 28 ER+ breast tumors using the Panomics QuantiGene Plex 2.0 assay system (Affymetrix; see paper Methods). H&E-stained, FFPE breast tumor samples exhibiting (B) high or (C) low levels of infiltrating immune cells are shown. Red arrows indicate small, darkly staining nuclei of leukocytes; blue arrows mark tumor cell nuclei. (D) Distributions of mean-centered metagene values (based on three representative genes, per metagene) are shown as a function of immune cell abundance (L = low; I/L = intermediate-low; I/H = intermediate-high; H = high). Box and whisker plot parameters and statistical method are the same as for (A).

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Nagalla et al. Genome Biology 2013 14:R34   doi:10.1186/gb-2013-14-4-r34