Log 2 ( Cy5/Cy3) of SSH Log 2 ( Cy5/Cy3) of cDNA niques, the subtraction efficiency can be readily evaluated. As shown in Figure 2 , the subtraction efficiency was determined by the rare presence of clones with equal hybridization intensities between the forward and reverse amplicons, and by the consistent exclusion of the housekeeping genes in the subtracted amplicons. The specificity was further confirmed by quantification of the differential gene expression between hepatoma and para-hepatoma The differentially expressed genes Figure 5 The differentially expressed genes. The genes differentially expression in human hepatoma were identified by either only the conventional cDNA microarray assays (26 genes) or SSH/microarray assays (658 genes), or both (43 genes). The results were derived from three pairs of hepatoma liver tissues with at least two-fold difference in gene expression and P < 0.01. APEG1, TTN, HTN1, MEST, EVL3,  VLDLR, MYOG, TNNI2, HOXC11, IGF2, AHSG, TTID,  BIRC1, PAFAH1B1, SYK, LMNA, TNFRSF11B, FALZ,  BMP1, ETS2, NRD1, CXCL1, JAG1, SEMA4G, HEY1,  ZNF22, CRMP1, TEAD4, IGFBP1, IGFBP3, IGFBP7,  PTGS1 , NEUGRIN, CUGBP1) related to the regulation of cell differentiation and embryonic development, and 59 genes (ASGR2, CAP2, RGS5, ITGB4BP, NCK1, EVL3,  PLCG2, EPHA7, IGF2, IFNGR2, AHSG, CAP1, PTPRF,  CXCL2, GNAI1, TGFBR1, NCSTN, DOK1, FRBB3, SYK,  MC1R, CD79B, CSNKIE, CD69, AVPR1A, GNB2L1,  ACVR1, BIRC2, FLT4, CXCL1, FAG1, PNOC, SLC9A3R1,  LANCL1, GNB3, ADORA2B, FGR, NCK1, RAB11A, PLCG2,  LOC91614, PRKAR1A, FLJ22595, ARF3, TYK2,  MAP3K7IP1, MC1R, TNFSF10, ARF4, VAV2, AVPR1A,  GNB2L1, MAPK10, STMN1, SNX17, ADORA2B, ECT2,  RGS5, IGFBP3 ) associated with signal transduction in response to extra-cellular proliferation and growth stimuli were found. Our findings that differentially expressed genes were related to multi-biological processes suggest the complexity of the molecular mechanisms for hepatocellular carcinogenesis.