Gene set enrichment analysis validates the hypothesis that the hemangiosarcoma gene set is involved in hypoxia, inflammation, and cancer. (A) Bar graph representing the number of gene sets that were enriched in hemangiosarcoma samples versus splenic hematoma samples. Each of 23 genes on the x-axis was present in the number of gene sets indicated on the y-axis (of 30 where FDR < 0.05). (B) Bar graph representing the direction and magnitude of change in expression for six representative genes (IL8, TIMP1, MAO, PDGFRβ, CD44, EPHA2), one invariant control (IL8Rβ) and two housekeeping controls (GAPDH, β-actin) relative to the expression in splenic hematomas. Data for each group (three splenic hematomas, 14 hemangiosarcoma cell lines, and three hemangiosarcoma tissues) passed quality assurance using Affymetrix algorithms provided in GeneData Expressionist Refiner. Probe signal levels were quantile-normalized and summarized using the GeneChip-Robust Multichip Averaging (GC-RMA) algorithm. Normalized files were imported into GeneData Expressionist Analyst so average expression values for each group, based on multiple-probe hybridization data, could be used in the comparisons.