Breast tumor-derived immune gene clusters differentiate specific leukocyte cell types. The breast tumor-derived immune gene clusters were analyzed in the pan-leukocyte expression dataset of Abbas et al. . Signal intensities of the probe sets comprising the tumor-immune metagenes were extracted by probe set ID from the normalized leukocyte expression profiles of the Abbas dataset and hierarchically clustered by Pearson correlation and average linkage clustering. Genes belonging to the three immune clusters identified in groups 977A and 977B are indicated by color (green: B/P Cluster; blue: T/NK Cluster; magenta: M/D Cluster) in the gene dendrogram (left) and to the right of the figure. Clustered array profiles are delineated by horizontal colored bars (at top of figure) and named according to immune cell type. Array experimental annotations are provided in Additional file 8. B/P: B cell/plasma cells; M/D: monocytes and dendritic cells; NK; natural killer; T/NK: T cell and natural killer cells.
Nagalla et al. Genome Biology 2013 14:R34 doi:10.1186/gb-2013-14-4-r34