A novel method of differential gene expression analysis using multiple cDNA libraries applied to the identification of tumour endothelial genes

Table 3 Comparison of methods with table 7 from Huminiecki and Bicknell (2000)

Gene	FDR q-value	Endothelial ESTs	Non-endothelial ESTs	Original Unigene ID
ECSM2	0.0000	9	0	Hs.30089
MMRN1	0.0000	5	0	Hs.268107
ECSM1	0.0002	4	0	Hs.13957
FABP4	0.0031	3	0	Hs.83213
RASIP1	0.3696	1	0	Hs.233955
RAMP2	-	0	0	Hs.155106
VWF	0.0000	27	1	Hs.110802
CD93 (ECSM3)	0.0022	4	1	Hs.8135
ROBO4 (ECSM4)	0.0022	4	1	Hs.111518
CDH5	0.0022	4	1	Hs.76206
EDN1	0.0000	7	2	Hs.2271
SDPR	0.0001	6	2	Hs.26530
PECAM1	0.0000	24	5	Hs.78146
EFEMP1	0.0000	40	8	Hs.76224
COL4A1	0.5598	4	16	Hs.119129
CTGF	0.0000	30	49	Hs.75511

Listing of the genes from Table 7 of our earlier work [8] and how they came out in the new analysis. 13 of the 16 genes were significantly endothelial; however, non-endothelial hits to known endothelial genes showed that the choice of non-endothelial cell lines could be improved. q-values in bold denote a significance threshold of <= 0.01.

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