Differential expression of 6 transcripts as measured by microarray and quantitative RT-PCR. The percentage of cases in 5-FU/LV (control) and 5-FU/LV + SU5416 trial arms with increased expression (at predose day 56 relative to predose day 1) of each transcript is displayed. Panel A displays results from Affymetrix analysis and Panel B displays results from SYBR Green RT-PCR verification. For the Affymetrix data, an increase is determined by Difference Call status; for the SYBR Green data, an increase is defined here as relative expression value of 2-fold or greater. A total of 31 sample pairs were used in RT-PCR analysis; 18 were from SU5416 arm (5 PR, 1 CR, 11 PD, and 1 SD response at end of cycle 1), and 13 were from the control arm (9 PR, 3 PD, and 1 SD). The relative expression values as determined in the RT-PCR analysis for each patient are displayed (see Additional File 1).