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Gene array analysis and the liver
Article first published online: 7 MAR 2007
DOI: 10.1002/hep.1840360603
Copyright © 2002 American Association for the Study of Liver Diseases
Additional Information
How to Cite
Shackel, N. A., Gorrell, M. D. and McCaughan, G. W. (2002), Gene array analysis and the liver. Hepatology, 36: 1313–1325. doi: 10.1002/hep.1840360603
Publication History
- Issue published online: 7 MAR 2007
- Article first published online: 7 MAR 2007
- Manuscript Accepted: 11 SEP 2002
- Manuscript Received: 14 JUN 2002
Funded by
- National Institutes of Health. Grant Number: RFA/DK/98.017
Reference
- 1, . Functional genomics: it's all how you read it. Science 1997; 278: 601–602.
- 2, , , . Serial analysis of gene expression. Science 1995; 270: 484–487.
- 3, , , . Subtractive hybridizationgenetic takeaways and the search for meaning. Int J Exp Pathol 2000; 81: 391–404.Direct Link:
- 4, , . Application of differential display to immunological research. J Imrnunol Methods 2001; 250: 29–43.
- 5, , . Expression profiling: DNA arrays in many guises. Bioessays 1999; 21: 781–790.Direct Link:
- 6, , , . Open systems: panoramic views of gene expression. J Immunol Methods 2001; 250: 67–79.
- 7. . Microarray technology-enhanced versatility, persistent challenge. Curr Opin Biotechnol 2000; 11: 36–41.
- 8, , , , . DNA microarray technology: the anticipated impact on the srudy of human disease. Biochim Biophys Acta 1999; 25: M17–28.
- 9, , , , , . Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol 1998; 16: 301–306.
- 10
- 11, , , , , . , et al. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Hum Mol Genet 1999; 8: 1715–1722.
- 12. Applications ofnylon membrane arrays to gene expression analysis. J Ininiunol Methods 2001; 250: 3–13.
- 13
- 14, , , . Importance of replication in microarray gene expresiion studies: staristical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 2000; 97: 9834–9839.
- 15
- 16, , , . High density synthetic oligonucleotide arrays. Nat Genet 1999; 21: 20–24.
- 17, , , , , , . et al. Expression monitoring by hybridization to higlidensity oligonuclcoride arrays. Nature Biotechnol 1996; 14: 1675–1680.
- 18, , , , . . Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. proc Natl Acad Sci USA 1996; 93: 13555–13560.
- 19, , . , . , , et al. Accessing genetic information with high-density DNA arrays. Science 1996; 274: 610–614.
- 20. , , , , . Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 1994; 91: 5022–5026.
- 21. When the chips are down. Nature 2001; 410: 860–861.
- 22, , , , , , , et al. The transcriptional program in the response ofhuman fibroblasts to serum. Science 1999; 283: 83–87.
- 23, , , , , , , et al. Activation changes the spectrum but not the diversity of genes expressed by T cells. Proc Nacl Acad Sci USA 1999; 96: 12691–12696.
- 24, , , . A reliable external control for ribonuclease protection assays. Nucleic Acids Res 1997; 25: 1305–1306.
- 25
- 26, , , , , . Assessment of rhe sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 2000; 28: 4552–4557.
- 27, , . , , , . Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc Natl Acad Sci USA 2000; 97: 3260–3265.
- 28, , , , , , , et al. Analysis of gene expression in single live neurons. Prof Natl Acad Sci USA 1992; 89: 3010–3014.
- 29, , . Gene expression profiling in the amygdala: An approach to examine the molecular substrates of mammalian behavior. Physiol Behav 2001; 73: 841–847.
- 30. Amplification of mRNA populations using aRNA generated from immobilized oligo(dT)-T7 primed cDNA. Biotechniques 1996; 20: 584–591.
- 31, . Construction of cDNA libraries from single cells. Meth Enzymol 1993; 225: 611–623.
- 32, , , . Detection of differentially regulated genes in keratinocytes by cDNA array hybridization: Hsp27 and other novel players in response to artificial ultraviolet radiation. J Invest Dermatol 2001; 116: 983–988.
- 33, , , , , . Reproducibility of alternative prohe synthesis approaches for gene expression profiling with arrays. J Mol Diagnostics 2000; 2: 124–127.
- 34. Use of SMART-generated cDNA for differential gene expression studies. J Mol Med 2000; 78:B23.
- 35, , , , , , , et al. Analysis of gene expression in human bullous keratopathy corneas containing limiting amounts of RNA. Invest Ophthalmol Vis Sci 1999; 40: 3108–3115.
- 36, , , , , , ,. SMART amplification maintains representation of relative gene expression: quantitative validation by real time PCR and application to studies ofalcoholic liver disease in primates. J Biochem Biophys Methods (in press).
- 37
- 38. Analysing gene expression data from DNA microarrays to identify candidate genes. J Pathol 2001; 195: 53–65.Direct Link:
- 39, , , , , . Identifying differentially expressed genes in cDNA microarray experiments. J Comput Biol 2001; 8: 639–659.
- 40, , , , , , . General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. J Biomed Optics 2000; 5: 411–424.
- 41, , , , , , . Multivariate measurement of gene expression relationships. Genomics 2000; 67: 201–209.
- 42, . Transcriptional profiling reveals global defects in energy metabolism, lipoprotein, and bile acid synthesis and transport with reversal by leptin treatment in obtob mouse liver. J Biol Chein 2001; 276: 49066–49076.
- 43, , , . Basic microarray analysis: grouping and feature reduction. Trends Biotechnol 2001; 19: 189–193.
- 44
- 45. Analysis of large-scale gene expression data. Curr Opin Immunol 2000; 12: 201–205.
- 46. Computational analysis of microarray data. Nat Rev Genet 2001; 2: 418–427.
- 47, , , , , , , et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000; 97: 262–267.
- 48, , , , , , , et al. The sequence ofthe human genome. Science 2001; 291: 1304–1351.
- 49, , , , , , , et al. Analysis of human transcriptomes. Nat Genet 1999; 23: 387–388.
- 50, . Molecular profiling of human cancer. Nat Rev Genet 2000; 1: 48–56.
- 51, , , , , , , et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000; 24: 227–235.
- 52, , , , , , , et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999; 286: 531–537.
- 53, , , , , , , et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000; 403: 503–511.
- 54, , , , , , , et al. Artificial neural networks distinguish among subtypes of neoplastic colorectal lesions. Gastroenterology 2002; 122: 606–613.
- 55, , , , . Identification of novel molecules and pathogenic pathways in primary biliary cirrhosis: cDNA array analysis of intrahepatic differential gene expression. Gut 2001; 49: 565–576.
- 56, , , , . Insights into the pathobiology of hepatitis C virus associated cirrhosis: analysis of intraheparic differential gene expression. Am J Pathol 2002; 160: 641–654.
- 57. , , , , , , et al. Real-time reverse trasncriprase-polyrnerase chain reaction (RT-PCR) for measurement of cytokine and growth factor mRNA expression with fluorogenic probes or SYBR Green I. Immunol Cell Biol 2001: 79: 213–221.Direct Link:
- 58, , , . Laser capture microscopy. Mol Pathol 2000; 53: 64–68.
- 59, , , , . Laser-capture microdissection: opening rhe microscopic frontier to molecular analysis. Trends Genet 1998; 14: 272–276.
- 60, . , . Multiple tissue core arrays in histopathology research: a validation study. J Pathol 2000; 192: 549–553.Direct Link:
- 61, . , , , . , et al. validation of tissue microarrays for immunohistochemical profiling of cancer specimens using the example of human fibroblastic tumors. Am J Pathol 2001; 158: 1245–1251.
- 62. , . DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J Virol 2001; 75: 7059–7066.
- 63, , , , , . Global changes in interleukin-6-dependent gene expression patterns in mouse livers after parrial hepatectomy. HEPATOLOGY 2001; 33: 1377–1386.Direct Link:
- 64, , , . Cluster analysis: and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998; 95: 14863–14868.
- 65, . , . . Differential genc cxprcssion between chronic hepatitis B and C hepatic lesions. Gastroenterology 2001; 120: 955–966.
- 66. . . Discussion on differential gene expression btrween chronic hepatitis B and C hepatic lesion. Gastroenterology 2001; 121: 1263–1264.
- 67
- 68, , . , . , , et al. Disease fingerprinting with cDNA microarrays reveals distinct gene expression profiles in lethal type 1 and type 2 cytokine-mediated inflammatory reactions. FASEB J 2001: 15: 2545–2547.
- 69. . . , . , . RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. HFPATOLOGY 2001; 33: 1239–1258.Direct Link:
- 70, , . . Genoniic profiling ofshortand long-term caloric restricrion effects in the liver of aging mice. Proc Natl Acad Sci USA 2001; 98: 10630–10635.
- 71, , , , . Independent and overlapping transcriptional activation during livrr development and regeneration in micc. HEPATOLOGY 2002: 35: 525–534.Direct Link:
- 72, . . . Project normal: defining normal variance in niouse gene expression. Proc Natl Acad Sci USA 2001; 98: 13266–13271.
- 73, . , , , , . Tempnral grne expression analysis of monolayer culturcd rat hepatocytes. Chem Res Toxicol 2001; 14: 1218–1231.
- 74, . , . , , . Implicarions of circadian gene expression in kidney, liver and thc effects of faxing on pharmacogenoinic studies. Pharmacogenecics 2002; 12: 55–65.
- 75, , , . The Diet1 locus confers protection against hypercholesrerolcmia through enhanced bile acid metabolism. J Biol Cheni 2002: 277: 469–477.
- 76, , . , , . , et al. Increased expression of rhc sterol regulatory elementbinding protein-1 gene in insulin receptor substrate-2(-/-) mouse liver. J Biol Cheni 2001; 276: 38337–38340.
- 77, , , , , . . The peroxisoine proliferator-activated receptor alpha regulates amino acid metabolism. FASEB J 2001; 15: 1971–1978.
- 78, , , , . Differenrial gene expression of livers from ApoE deficient mice. Life Sci 2000; 68: 19–28.
- 79, , , . . Microarray expression profiling identifies genes with altered expression in HDL-dcficienr mice. Genome Res 2000: 10: 2022–2029.
- 80, , , , , , . Diet-induced obeslty and hepatic gene expression alteration in C57BI/6J and ICAM-1-deficient mice. Am J Physiol Endocrinol Metab 2002; 282: F703–713.
- 81, , , , , . Effect of selenium and vitamin E deficiency on diffcrcntial gene expression in rat liver. Biochcm Biophys Res Commun 2001; 285: 470–475.
- 82, , , . , , . Target gene search for the metal-responsive transcription factor MTF-1. Nucleic Acids Kes 2001: 29: 1514–1523.
- 83, . , . Transgenic targeting of a dominant negative corepressor to liver blocks basal repression by thyroid hormone receptor and incrrases cell proliferation. J Biol Chem 2001: 276: 15066–15072.
- 84. , , . Thyroid hormone regulation of hepatic genes in vivo detected by complementary DNA microarray. Mol Endocrinol 2000; 14: 947–955.
- 85, , , , , , , et al. Interferon-alpha activates multiple STAT signals and down-regulates c-Met in primary human hepatocytes. Gastroenterology 2002; 122: 1020–1034.
- 86, , , , . Immortal activated human hepatic stellare cells generated by ectopic relomerase expression. Lab Invest 2002; 82: 323–333.
- 87. . , , , . Increased levels of forkhead box M 1 B transcription factor in transgenic mouse hepatocytes prevent age-related proliferation defects in regenerating liver. Proc Natl Acad Sci USA 2001; 98: 11468–11473.
- 88, , . , , , , et al. Methionine adenosyltransferase IA knockout mice are predisposed to liver injury and exhibit increased expression of genes involved in proliferation. Proc Natl Acad Sci USA 2001; 98: 5560–5565.
- 89, , . Identification ofgenes induced by growth hormorie in rat liver using cDNA arrays. Endocrinology 2000; 141: 4321–4324.
- 90. . , , , , . 0(2)-Vinyl 1-(pyrrolidin-1-yl)diazen-l-ium-l,2-diolate protection against D-galactosaminelendotoxin-induced hepatotoxicity in mice: gcnomic analysis using microarrays. J Pharmacol Exp Ther 2002; 300: 18–25.
- 91, , , , , , . Expression profiling of acetaminophen liver toxicity in mice usins microarray technology. Biochem Biophys Res Commun 2001; 282: 321–328.
- 92, , . Microarray analysis of gene expres sion changes in niousc liver induced by peroxisome proliferator-activated receptor alpha agonists. Biochem Biophys Res Commun 2002; 290: 1114–1122.
- 93, , , , , , , et al. Diverse roles of rhe nuclear orphan receptor CAR in regulating hepatic genes in response to phenobarbital. Mol Pharniacol 2002; 61: 1–6.
- 94, , , , , , , et al. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol Appl Pharmacol 2001; 175: 28–42.
- 95, , , , , . Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol Genomics 2001; 5: 161–170.
- 96, , , , . Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett 2001; 120: 359–368.
- 97. , . . Genetic events associated with arsenic-induced malignanr transformation: applications of cDNA microarray technology. Mol Carcinog 2001; 30: 73–87.Direct Link:
- 98, , . Applications of gene arrays in environmcntal toxicology: fingerprints ofgene regulation associated with cadmium chloride, benzo(a)pyrene. and trichloroethylene. Environ Health Perspect 2001; 109: 71–74.
- 99
- 100, , , , , . Identification of a possible association between carbon tetrachloridc-induced hepatotoxicity and interleukin-8 expression. J Biochcm Mu1 Toxicol 2000; 14: 283–290.Direct Link:
- 101, , , , . Developmcnt of a toxicological gene array and quantirative assessment of this technology. Arch Biocheni Biophys 2000; 376: 66–73.
- 102, , , , . Gene microarray analysis reveals a novel hypoxia signal transduction pathway in human hepatocellular carcinoma cells. Int J Oncol 2001; 19: 129–135.
- 103, , , , , . Upstream binding factor up-regulated in hepatocellular carcinoma is related to the survival and cisplatin-sensitivity of cancer cells. FASEB J 2002; 16: 293–301.
- 104, , , , , , , et al. Insighr into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma wirh those of corresponding noncancerous liver. Proc Natl Acad Sci USA 2001; 98: 15089–15094.
- 105, , , , , , , et al. Genome-wide screening of genes showing altered expression in liver metastases of human colorectal cancers by cDNA microarray. Neoplasia 2001; 3: 395–401.
- 106, , , , , , , et al. Examination of oncogene amplification by genomic DNA microarray in hepatocellular carcinomas: comparison with comparative genomic hybridization analysis. Cancer Genet Cytogenet 2001; 130: 127–132.
- 107, . , , . cDNA arrays and immunohistochemistry identification of CD10/CALLA expression in hepatocellular carcinoma. Am J Pathol 2001; 159: 1415–1421.
- 108, , , , , , , et al. Identification of differentially expressed genes in hepatocellular carcinoma and metastatic liver tumors by oligonucleotide expression profiling. Cancer 2001; 92: 395–405.Direct Link:
- 109, , , , , , , et al. Expression profiling suggested a regulatory role ofliver-enriched transcription factors in human hepatocellular carcinoma. Cancer Res 2001; 61: 3176–3181.
- 110, , , , . Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. HEPATOLOGY 2001; 33: 832–840.Direct Link:
- 111. , , , , , , et al. Genome-wide analysis of gene expression in human heparocellular carcinomas using cDNA microarray: identification ofgenes involved in viral carcinogenesis and tumor progression. Cancer Res 2001; 61: 2129–2137.
- 112, , , , . a-Fetoproteinproducing hepatoma cell lines share common expression profiles of genes in various categories demonstrated by cDNA microarray analysis. HEPATOLOGY 2001; 33: 676–691.Direct Link:
- 113, , , , , , , et al. Differential gene expression of hepatocellular carcinoma using cDNA microarray analysis. Oncol Res 2000; 12: 59–69.
- 114, , , , , , . Distinctive gene expression profiles associated with hepatitis B virus x protein. Oncogene 2001; 20: 3674–3682.
- 115, , , . Selective transcriptional regulations in the human liver cell by hepatitis B viral X protein. Biochem Biophys Res Commun 2000; 272: 525–530.
- 116, , , , , , , et al. A human hepatoma cell line expressing hepatitis C virus nonstructural proteins tightly regulated by tetracycline. Biochem Biophys Res Commun 2001; 281: 732–740.
- 117, , . Profiling of genes which are differentially expressed in mouse liver in response to adenoviral vectors and delivered genes. Gene Ther 2000; 7: 903–909.
- 118, , , , , , , et al. A protective role for cyclooxygenase-2 in drug-induced liver injury in mice. Chem Res Toxicol 2001; 14: 1620–1628.
- 119, , , , , , , et al. Acetyl-coenzyme A synthetase is a lipogenic enzyme controlled by SREBP-1 and energy status. Am J Physiol Endocrinol Metab 2002; 282: E222–230.
- 120, , , , , , , et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999; 96: 2907–2912.

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