Table 1. Comparison between 3′IVT microarray with FDR<0.001 and exon array gene expression fold change levels.

Comparison groups	No. of total differentiallyexpressed genesidentified with 3′IVT array	No. of common differentially expressed genes found in the comparison exonarray versus 3′IVT array (%)
		Full probe level	Extended probe level	Core probe level
Dysplasia vs Transgenic	95	68 (71.58%)	68 (71.58%)	63 (66.32%)
Dysplasia vs Non-transgenic	237	157 (66.24%)	155 (65.40%)	129 (54.43%)
Tumor vs Transgenic	359	283 (78.83%)	275 (76.60%)	239 (66.57%)
Tumor vs Non-transgenic	404	337 (83.42%)	332 (82.18%)	292 (72.28%)

Number of common genes found in comparison between 3′IVT and exon array. For 3′IVT array differential gene expression fold change obtained using ArrayTrack software with parameters as false detection rate (FDR) <0.001, fold change of ≥2, mean channel intensity (MCI) of 100, bad flag of 5. For exon array differential gene expression fold change obtained using Biotique XRAY software at p<0.05 using a minimum probeset per gene of 2 and a minimum of 2 probes per probeset. In the () are % of genes found common in exon array from 3′IVT array.