List of 34 HCC specific genes: comparison of gene expression data from the Liverome database and experimental dataset.

Expression trend of 34 HCC specific genes reported as deregulated in more than 4 studies in the public Liverome database was compared to experimental expression trend.
aaverage rate of expression from different Illumina probes.
bdiscrepancies between Liverome studies results.
Table 3 References.
1) Chan, K.Y., Lai, P.B., Squire, J.A., Beheshti, B., Wong, N.L., Sy, S.M., Wong, N., 2006. Positional expression profiling indicates candidate genes in deletion hotspots of hepatocellular carcinoma. Mod Pathol 19, 1546–1554.
2) Chung, E.J., Sung, Y.K., Farooq, M., Kim, Y., Im, S., Tak, W.Y., Hwang, Y.J., Kim, Y.I., Han, H.S., Kim, J.C., Kim, M.K., 2002. Gene expression profile analysis in human hepatocellular carcinoma by cDNA microarray. Mol Cells 14, 382–387.
3) Cui, X.D., Lee, M.J., Yu, G.R., Kim, I.H., Yu, H.C., Song, E.Y., Kim, D.G., 2010. EFNA1 ligand and its receptor EphA2: potential biomarkers for hepatocellular carcinoma. Int J Cancer 126, 940–949.
4) De Giorgi, V., Monaco, A., Worchech, A., Tornesello, M., Izzo, F., Buonaguro, L., Marincola, F.M., Wang, E., Buonaguro, F.M., 2009. Gene profiling, biomarkers and pathways characterizing HCV-related hepatocellular carcinoma. J Transl Med 7, 85.
5) Delpuech, O., Trabut, J.B., Carnot, F., Feuillard, J., Brechot, C., Kremsdorf, D., 2002. Identification, using cDNA macroarray analysis, of distinct gene expression profiles associated with pathological and virological features of hepatocellular carcinoma. Oncogene 21, 2926–2937.
6) Dong, H., Ge, X., Shen, Y., Chen, L., Kong, Y., Zhang, H., Man, X., Tang, L., Yuan, H., Wang, H., Zhao, G., Jin, W., 2009. Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE. BMC Med Genomics 2, 5.
7) Goldenberg, D., Ayesh, S., Schneider, T., Pappo, O., Jurim, O., Eid, A., Fellig, Y., Dadon, T., Ariel, I., de Groot, N., Hochberg, A., Galun, E., 2002. Analysis of differentially expressed genes in hepatocellular carcinoma using cDNA arrays. Mol Carcinog 33, 113–124.
8) Iizuka, N., Tsunedomi, R., Tamesa, T., Okada, T., Sakamoto, K., Hamaguchi, T., Yamada-Okabe, H., Miyamoto, T., Uchimura, S., Hamamoto, Y., Oka, M., 2006. Involvement of c-myc-regulated genes in hepatocellular carcinoma related to genotype-C hepatitis B virus. J Cancer Res Clin Oncol 132, 473–481.
9) Kato, K., Yamashita, R., Matoba, R., Monden, M., Noguchi, S., Takagi, T., Nakai, K., 2005. Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res 33, D533–536.
10) Kim, B.Y., Lee, J.G., Park, S., Ahn, J.Y., Ju, Y.J., Chung, J.H., Han, C.J., Jeong, S.H., Yeom, Y.I., Kim, S., Lee, Y.S., Kim, C.M., Eom, E.M., Lee, D.H., Choi, K.Y., Cho, M.H., Suh, K.S., Choi, D.W., Lee, K.H., 2004. Feature genes of hepatitis B virus-positive hepatocellular carcinoma, established by its molecular discrimination approach using prediction analysis of microarray. Biochim Biophys Acta 1739, 50–61.
11) Kurokawa, Y., Matoba, R., Takemasa, I., Nakamori, S., Tsujie, M., Nagano, H., Dono, K., Umeshita, K., Sakon, M., Ueno, N., Kita, H., Oba, S., Ishii, S., Kato, K., Monden, M., 2003. Molecular features of non-B, non-C hepatocellular carcinoma: a PCR-array gene expression profiling study. J Hepatol 39, 1004–1012.
12) Lee, M.J., Yu, G.R., Park, S.H., Cho, B.H., Ahn, J.S., Park, H.J., Song, E.Y., Kim, D.G., 2008. Identification of cystatin B as a potential serum marker in hepatocellular carcinoma. Clin Cancer Res 14, 1080–1089.
13) Li, Y., Tang, R., Xu, H., Qiu, M., Chen, Q., Chen, J., Fu, Z., Ying, K., Xie, Y., Mao, Y., 2002. Discovery and analysis of hepatocellular carcinoma genes using cDNA microarrays. J Cancer Res Clin Oncol 128, 369–379.
14) Okabe, H., Satoh, S., Kato, T., Kitahara, O., Yanagawa, R., Yamaoka, Y., Tsunoda, T., Furukawa, Y., Nakamura, Y., 2001. Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression. Cancer Res 61, 2129–2137.
15) Patil, M.A., Chua, M.S., Pan, K.H., Lin, R., Lih, C.J., Cheung, S.T., Ho, C., Li, R., Fan, S.T., Cohen, S.N., Chen, X., So, S., 2005. An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma. Oncogene 24, 3737–3747.
16) Shirota, Y., Kaneko, S., Honda, M., Kawai, H.F., Kobayashi, K., 2001. Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Hepatology 33, 832–840.
17) Tackels-Horne, D., Goodman, M.D., Williams, A.J., Wilson, D.J., Eskandari, T., Vogt, L.M., Boland, J.F., Scherf, U., Vockley, J.G., 2001. Identification of differentially expressed genes in hepatocellular carcinoma and metastatic liver tumors by oligonucleotide expression profiling. Cancer 92, 395–405.
18) Xu, L., Hui, L., Wang, S., Gong, J., Jin, Y., Wang, Y., Ji, Y., Wu, X., Han, Z., Hu, G., 2001a. Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma. Cancer Res 61, 3176–3181.
19) Xu, X.R., Huang, J., Xu, Z.G., Qian, B.Z., Zhu, Z.D., Yan, Q., Cai, T., Zhang, X., Xiao, H.S., Qu, J., Liu, F., Huang, Q.H., Cheng, Z.H., Li, N.G., Du, J.J., Hu, W., Shen, K.T., Lu, G., Fu, G., Zhong, M., Xu, S.H., Gu, W.Y., Huang, W., Zhao, X.T., Hu, G.X., Gu, J.R., Chen, Z., Han, Z.G., 2001b. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc Natl Acad Sci U S A 98, 15089–15094.
20) Yamashita, T., Kaneko, S., Hashimoto, S., Sato, T., Nagai, S., Toyoda, N., Suzuki, T., Kobayashi, K., Matsushima, K., 2001. Serial analysis of gene expression in chronic hepatitis C and hepatocellular carcinoma. Biochem Biophys Res Commun 282, 647–654.
21) Zekri, A.R., Hafez, M.M., Bahnassy, A.A., Hassan, Z.K., Mansour, T., Kamal, M.M., Khaled, H.M., 2008. Genetic profile of Egyptian hepatocellular-carcinoma associated with hepatitis C virus Genotype 4 by 15 K cDNA microarray: preliminary study. BMC Res Notes 1, 106.