Supplementary Table 2.

Comparison with other RCC studies.

	Method	number of samples/microarray platform	Final number of genes	Overlap with 158 marker genes	Overlap with 64* marker-genes
Young et al. 2001	More than two-fold changed in two or more tumor samples	7 tumor (4 cc-RCC), 7 normal/cDNA 7,075 genes	189	8	1
Takahashi et al. 2001	Three-fold or more changed in 75% or more of the tumor samples	29 cc-RCC and 29 normal/cDNA 21,632 genes	109	7	-
Gieseg et al. 2002	Changed genes in cc-RCC with Wilcoxon test p-value ≤0.001 and fold change ≥1.1	13 RCC (9cc-RCC), 9 normal/ Affymetrix 5600 genes	355 genes, 85 reported	4	1
Boer et al. 2001	adapted sign test by counting for each gene the number of times that its measured intensity in the set of repeated pair-wise comparisons is higher in T and N	37 cc-RCC, 37 normal	1738 cDNAs	45	11
Higgins et al. 2003	No reported gene set; selected genes with avg fold change >3 and t-test p-value >0.03.	41 RCC (23 cc-RCC), 3 normal/cDNA 22,648 genes	182 genes	8	1
Jones et al. 2005	90% lower confidence boung of the fold change was >2 and t-test p-value <0.001	8 clear cell stage I, 23 normal, Affymetrix 22,283 genes	1359 up-regulated, 493 down-regulated	37 up, 19 down-regulated	15 up-regulated
Sultmann et al. 2005	t-test with estimated false discovery rate <0.23	25 ccRCC, 25 normal/RCC-specific cDNA microarrays with 4207 genes	620 up-regulated; 561 down-regulated genes	13 up, 11 down-regulated	5 up, 2 down-regulated

^*genes not identified by Lenburg et al.