Table IV.

Comparison of GeneChip array data to qRT-PCR results of selected genes in original study samples and replication set

		Original sample set				Replication set
Gene symbol	Gene name	Array Fold change*	qRT-PCR Fold change†	P value‡	Correlation§	qRT-PCR Fold change||	P value‡
TLR2	Toll like receptor 2	2.1	3.1	0.0558	0.68	3.1	0.0194
IL8	Interleukin 8	18.4 4.9	10.1	0.0011	0.92 0.87	N/A	N/A
CXCL1	Chemokine (C-X-C motif) ligand 1	5.7	6.6	0.0002	0.93	2.8	0.0140
CXCL2	Chemokine (C-X-C motif) ligand 2	6.5	5.9	0.0028	0.88	5.3	0.0009
CXCL3	Chemokine (C-X-C motif) ligand 3	6.5	7.1	0.0003	0.87	4.0	0.0033
IL6	Interleukin 6	4.9	10.0	0.0017	0.92	4.6	0.0072
CCL20	Chemokine (C-X-C motif) ligand 20	5.3	23.4	0.0003	0.91	10.1	0.0009
PBEF	Pre-B-cell colony-enhancing factor	2.1 1.9	3.6	0.0062	0.80 0.78	2.3	0.0265

^*Fold change represents the average increase in 13 new TIL samples relative to 12 new TNL samples.

^†Fold change refers to expression change in TIL relative to TNL. There are 2 probe sets for IL8 and PBEF on the GeneChip.

^‡The P values were calculated using a Wilcoxon rank sum test comparing TIL samples with their TNL counterparts.

^§Correlation indicates the Pearson correlation coefficient between 9 TIL and 9 TNL samples for which both array and qRT-PCR measurements exist (P < 0.0001). Two correlation coefficients appear for IL8 and PBEF because each of these genes is represented by 2 probe sets on the array.

^||Comparison was between 9 TIL and 9 TNL samples.