ArticleBMC medical genomics2009
Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE.
Article in BMC medical genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 28 citations in OpenAlex.
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- Identification of potential key genes and high-frequency mutant genes in prostate cancer by using RNA-Seq data.Oncology letters · 2018Article
- DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates.Bioinformatics (Oxford, England) · 2017Article
- miR-122-mediated translational repression of PEG10 and its suppression in human hepatocellular carcinoma.Journal of translational medicine · 2016Article
- Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.BMC genomics · 2015Article
- Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.PloS one · 2013Article
- Identification of novel gene targets and functions of p21-activated kinase 1 during DNA damage by gene expression profiling.PloS one · 2013Article
- Cyr61/CCN1 is regulated by Wnt/β-catenin signaling and plays an important role in the progression of hepatocellular carcinoma.PloS one · 2012Article
- Digital karyotyping reveals probable target genes at 7q21.3 locus in hepatocellular carcinoma.BMC medical genomics · 2011Article
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- Characterization of conserved and nonconserved imprinted genes in swine.Biology of reproduction · 2009Article
Corrections and comments
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Authors and funding
12 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHepatocellular carcinoma (HCC) is one of the most common cancers worldwide and the second cancer killer in China. The initiation and malignant transformation of cancer result from accumulation of genetic changes in the sequences or expression level of cancer-related genes. It is of particular importance to determine gene expression profiles of cancers on a global scale. SAGE and LongSAGE have been developed for this purpose.
methodsWe performed SAGE in normal liver and HCC samples as well as the liver cancer cell line HepG2. Meanwhile, the same HCC sample was simultaneously analyzed using LongSAGE. Computational analysis was carried out to identify differentially expressed genes between normal liver and HCC which were further validated by real-time quantitative RT-PCR.
resultsApproximately 50,000 tags were sequenced for each of the four libraries. Analysis of the technical replicates of HCC indicated that excluding the low abundance tags, the reproducibility of SAGE data is high (R = 0.97). Compared with the gene expression profile of normal liver, 224 genes related to biosynthesis, cell proliferation, signal transduction, cellular metabolism and transport were identified to be differentially expressed in HCC. Overexpression of some transcripts selected from SAGE data was validated by real-time quantitative RT-PCR. Interestingly, sarcoglycan-epsilon (SGCE) and paternally expressed gene (PEG10) which is a pair of close neighboring genes on chromosome 7q21, showed similar enhanced expression patterns in HCC, implicating that a common mechanism of deregulation may be shared by these two genes.
conclusionOur study depicted the expression profile of HCC on a genome-wide scale without the restriction of annotation databases, and provided novel candidate genes that might be related to HCC.
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