Figure 3

(A) (Left panel) percent of transcripts whose expression correlates with its respective copy number in different sets of genes ranked in .1 decrements of correlation (y value) in expression between CMs and TMs; significant correlation between RNA expression and DNA copy number set at a Pearson's correlation cutoff p-value of < 0.05. The number of genes included in each gene set is shown in the right panel. (B) Venn diagram displaying the number of transcripts among the complete genome whose expression is consistent between CMs and TMs and correlates with copy number. (C) Bar graph demonstrating the top biological functions of the 968 target genes analyzed with Ingenuity Pathway Analysis www.ingenuity.com. (D) Top: Chromosomal view of the location of the 968 target genes mapped to their location within the genome. Copy number states are shown per sample for amplifications (red), deletions (blue), and unchanged regions (green); Bottom: Histogram depicting the number of the 968 target genes per chromosome. (E) - Self organizing clustering of CMs and TMs based on the 968 delegate transcripts. Sample ID refers to the patients from whom either CMs or TMs were derived. A, B and C refer to TARA's classification as discussed in the text.