title: An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma.
abstract: Hepatocellular carcinoma (HCC) is one of the major causes of cancer deaths worldwide. New diagnostic and therapeutic options are needed for more effective and early detection and treatment of this malignancy. We identified 703 genes that are highly expressed in HCC using DNA microarrays, and further characterized them in order to uncover novel tumor markers, oncogenes, and therapeutic targets for HCC. Using Gene Ontology annotations, genes with functions related to cell proliferation and cell cycle, chromatin, repair, and transcription were found to be significantly enriched in this list of highly expressed genes. We also identified a set of genes that encode secreted (e.g. GPC3, LCN2, and DKK1) or membrane-bound proteins (e.g. GPC3, IGSF1, and PSK-1), which may be attractive candidates for the diagnosis of HCC. A significant enrichment of genes highly expressed in HCC was found on chromosomes 1q, 6p, 8q, and 20q, and we also identified chromosomal clusters of genes highly expressed in HCC. The microarray analyses were validated by RT-PCR and PCR. This approach of integrating other biological information with gene expression in the analysis helps select aberrantly expressed genes in HCC that may be further studied for their diagnostic or therapeutic utility.
authors.affiliation: Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA.
authors.forename: Mohini A
authors.initials: MA
authors.lastname: Patil
authors.forename: Mei-Sze
authors.initials: MS
authors.lastname: Chua
authors.forename: Kuang-Hung
authors.initials: KH
authors.lastname: Pan
authors.forename: Richard
authors.initials: R
authors.lastname: Lin
authors.forename: Chih-Jian
authors.initials: CJ
authors.lastname: Lih
authors.forename: Siu-Tim
authors.initials: ST
authors.lastname: Cheung
authors.forename: Coral
authors.initials: C
authors.lastname: Ho
authors.forename: Rui
authors.initials: R
authors.lastname: Li
authors.forename: Sheung-Tat
authors.initials: ST
authors.lastname: Fan
authors.forename: Stanley N
authors.initials: SN
authors.lastname: Cohen
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.forename: Samuel
authors.initials: S
authors.lastname: So
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D017403:In Situ Hybridization; D008113:Liver Neoplasms / Q000235:genetics*; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D014408:Biomarkers, Tumor