A total of 69 and 701 genes differentially expressed in human hepatoma were finally identified (based on the data derived from the three tissue pairs in duplicate with log 2 > 1 or < -1, and P < 0.01) by the regular cDNA microarray assays and by the SSH/microarray assays, respec-tively ( Figure 5 & see additional file 1). That is, the SSH/ microarray assays detected 10-fold more differentially expressed genes, particularly for those low-expression genes, than did the conventional cDNA microarray. To confirm the differential expression of genes with low expression identified by the SSH/microarray assays (including 446 and 255 up-and down-regulated genes, respectively), we quantified the relative expression level of nine randomly selected genes, whose differential expression was detected by the SSH/microarray assays, in 18 pairs of HCC and the matched non-HCC liver tissues. We found the results were consistent with those obtained from SSH/microarray assays ( Figure 6 ).