Additional file 7.

Figure S3 - Concordance among gene clusters derived from patient groups 977A and 977B. (A) Expression patterns of probes comprising the proliferation (P) and immune clusters (IC) were compared between 977A and 977B. All selected probes (n = 210) and tumors (n = 1,954) were hierarchically clustered, then the tumors were partitioned (in cluster order) by patient group. Genes comprising the proliferation and immune clusters are distinguished by color according to the key shown. (B) Proliferation and immune cluster metagene values (ie, averaged log2 signal intensities; see Methods), derived from 977A and 977B, were compared to one another by Pearson correlation. Pearson coefficients (r) are represented by heatmap and described by the color key. r values corresponding to the cognate clusters are shown in white font. Biological titles equated with the immune clusters elsewhere in the manuscript are shown for continuity.

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