Fig. 1

Down-regulation of pro- and anti-angiogenic ligands in primary prostate tumors. a-d: VEGFA (a), PGF (b), and the receptor gene KDR (c) are expressed at lower levels in prostate tumors than in normal prostate tissue in the TCGA dataset, as shown by the density plots (top), box plots (middle), and spike plots (bottom). The co-receptor gene NRP1 (d) is expressed at slightly higher levels in tumors but has a similar overall distribution to normal tissues. e-h: This contrasts with the TCGA renal cell carcinoma (kidney) dataset, where VEGFA (e), PGF (f), KDR (g), and NRP1 (h) are heavily up-regulated in tumors. i VEGFA down-regulation in primary prostate cancer is observed across TCGA and microarray datasets, as is consistent down-regulation of class three semaphorins. The number in the boxes indicates the two-tailed t-test p-value after multiple testing correction with the Benjamini-Hochberg procedure. Only comparisons with corrected p-values less than 0.05 are displayed. The colors of the boxes indicate the magnitude of the t-statistic. The blue boxes to the right of the rows indicate that a gene is significantly down-regulated in two or more datasets with no significant differences in other datasets