• 1
    Aravind L. Guilt by association: contextual information in genome analysis. Genome Res 2000; 10: 10741077.
  • 2
    Vidal M. A biological atlas of functional maps. Cell 2001; 104: 333339.
  • 3
    Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M. Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J Mol Biol 2001; 314: 10531066.
  • 4
    Holloway AJ, van Laar RK, Tothill RW, Bowtell DDL. Options available—from start to fisnish—for obtaining data from DNA microarrays II. Nat Genet 2002; 32( Suppl): 481489.
  • 5
    Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, et al. A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 2001; 106: 413415.
  • 6
    Wong GKS, Passey DA, Yu J. Most of the human genome is transcribed. Genome Res 2001; 11: 19751977.
  • 7
    Quackenbush J. Computational analysis of microarray data. Nat Rev Genet 2001; 2: 418427.
  • 8
    Wright AF, van Heyningen V. Short cut to disease genes. Nature 2001; 414: 705706.
  • 9
    Arias IM, Boyer JL, Fausto N, Jakoby WB, Schachter DA, Shafritz DA. The liver. Biology and Pathobiology. 3rd ed. New York: Raven Press, 1994.
  • 10
    MacSween RNM, Burt AD, Portmann BC, Ishak KG, Scheuer PJ, Anthony PP. Pathology of the Liver. 4th ed. Orlando: Harcourt Brace, 2001.
  • 11
    Craig Barton M, Stivers DN. Microarray analysis of hepatic-regulated gene expression: specific applications and nonspecific problems. HEPATOLOGY 2002; 35: 727729.
  • 12
    Shackel NA, Gorrell MD, McCaughan GW. Gene array analysis and the liver. HEPATOLOGY 2002; 36: 13131325.
  • 13
    Olivier E, Soury E, Risler JL, Smih F, Schneider K, Lochner K, Jouzeau JY, et al. A novel set of hepatic mRNAs preferentially expressed during an acute inflammation in rat represents mostly intracellular proteins. Genomics 1999; 57: 352364.
  • 14
    Ruminy P, Gangneux C, Claeyssens S, Scotte M, Daveau M, Salier JP. Gene transcription in hepatocyte during the acute phase of a systemic inflammation: from transcription factors to target genes. Inflamm Res 2001; 50: 383390.
  • 15
    Anderson NL, Anderson NG. The human plasma proteome. History, character, and diagnostic prospects. Mol Cell Proteomics 2002; 1: 845867.
  • 16
    Yoo JY, Desiderio S. Innate and acquired immunity intersect in a global view of the acute-phase response. Proc Natl Acad Sci U S A 2003; 100: 11571162.
  • 17
    Masson S, Daveau M, Francois A, Bodenant C, Hiron M, Teniere P, Salier JP, et al. Up-regulated expression of HGF in rat liver cells after experimental endotoxemia: a potential pathway for enhancement of liver regeneration. Growth Factors 2001; 18: 237250.
  • 18
    Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics 2000; 2: 143147.
  • 19
    Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, et al. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 2000; 28: 316319.
  • 20
    Novak JP, Sladek R, Hudson TJ. Characterization of variability in large-scale gene expression data: implications for study design. Genomics 2002; 79: 104113.
  • 21
    Ihaka R, Gentleman RR. A language for data analysis and graphics. J Comput Graph Stat 1996; 5: 299314.
  • 22
    Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998; 95: 1486314868.
  • 23
    Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat Genet 2001; 29: 365371.
  • 24
    Lercher MJ, Urrutia AO, Hurst LD. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002; 31: 180183.
  • 25
    Colantuoni C, Henry G, Zeger S, Pevsner J. Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts. BioTechniques 2002; 32: 13161320.
  • 26
    Firestein GS, Pisetsky DS. DNA microarrays: boundless technology or bound by technology? Guidelines for studies using microarray technology. Arthritis Rheum 2002; 46: 859861.
  • 27
    Harbrecht BG, Billiar TR, Curran RD. Experimental models for studying the interaction of Kuppfer cells and hepatocytes. In: BilliarTR, CurranRD, eds. Hepatocyte and Kupffer Cell Interactions. Boca Raton, FL: CRC Press, 1992: 5570.
  • 28
    Chinnaiyan AM, Huber-Lang M, Kumar-Sinha C, Barrette TR, Shankar-Sinha S, Sarma VJ, Padgaonkar VA, et al. Molecular signatures of sepsis: multiorgan gene expression profiles of systemic inflammation. Am J Pathol 2001; 159: 11991209.
  • 29
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, et al. Gene ontology: tool for the unification of biology. Nat Genet 2000; 25: 2529.
  • 30
    Soury E, Olivier E, Simon D, Ruminy P, Kitada K, Hiron M, Daveau M, et al. Chromosomal assignments of mammalian genes with an acute inflammation-regulated expression in liver. Immunogenetics 2001; 53: 634642.
  • 31
    Welsh JB, Sapinoso LM, Kern SG, Brown DA, Liu T, Bauskin AR, Ward RL, et al Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum. Proc Natl Acad Sci U S A 2003; 100: 34103415.
  • 32
    Kim OS, Park EJ, Joe EH, Jou I. JAK-STAT signalling mediates gangliosides-induced inflammatory response in brain microglial cells. J Biol Chem 2002; 277: 4059440601.
  • 33
    Medzhitov R, Janeway CA Jr. Decoding the patterns of self and nonself by the innate immune system. Science 2002; 296: 298300.
  • 34
    Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 2002; 99: 44654470.
  • 35
    Bigger CB, Brasky KM, Lanford RE. DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J Virol 2001; 75: 70597066.
  • 36
    Okabe H, Satoh S, Kato T, Kitahara O, Yanagawa R, Yamaoka Y, Tsunoda T, et al. 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 2001; 61: 21292137.
  • 37
    Yano N, Habib NA, Fadden KJ, Yamashita H, Mitry R, Jauregui H, Kane A, et al. Profiling the adult human liver transcriptome: analysis by cDNA array hybridization. J Hepatol 2001; 35: 178186.
  • 38
    Cao SX, Dhahbi JM, Mote PL, Spindler SR. Genomic profiling of short- and long-term caloric restriction effets in the liver of aging mice. Proc Natl Acad Sci U S A 2001; 98: 1063010635.
  • 39
    Graveel CR, Jatkoe T, Madore SJ, Holt AL, Farnham PJ. Expression profiling and identification of novel genes in hepatocellular carcinomas. Oncogene 2001; 20: 27042712.
  • 40
    Shih DQ, Bussen M, Sehayek E, Ananthanarayanan M, Shneider BL, Suchy FJ, Shefer S, et al. Hepatocyte nuclear factor-1 alpha is an essential regulator of bile acid and plasma cholesterol metabolism. Nat Genet 2001; 27: 375382.
  • 41
    Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, et al. Gene expression patterns in human liver cancers. Mol Biol Cell 2002; 13: 19291939.
  • 42
    Iizuka N, Oka M, Yamada-Okabe H, Mori N, Tamesa T, Okada T, Takemoto N, et al. Comparison of gene expression profiles between hepatitis B virus- and hepatitis C virus-infected hepatocellular carcinoma by oligonucleotide microarray data on the basis of a supervised learning method. Cancer Res 2002; 62: 39393944.
  • 43
    Kelley-Loughnane N, Sabla GE, Ley-Ebert C, Aronow BJ, Bezerra JA. Independent and overlapping transcriptional activation during liver development and regeneration in mice. HEPATOLOGY 2002; 35: 525534.
  • 44
    Chuma M, Sakamoto M, Yamazaki K, Ohta T, Ohki M, Asaka M, Hirohashi S. Expression profiling in multistage hepatocarcinogenesis: identification of HSP70 as a molecular marker of early hepatocellular carcinoma. HEPATOLOGY 2003; 37: 198207.
  • 45
    Ye QH, Qin LX, Forgues M, He P, Kim JW, Peng AC, Simon R, et al. Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med 2003; 9: 416423.
  • 46
    Xu L, Hui L, Wang S, Gong J, Jin Y, Wang Y, Ji Y, et al. Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma. Cancer Res 2001; 61: 31763181.
  • 47
    Eickhoff H, Schuchhardt J, Ivanov I, Meier-Ewert S, O'Brien J, Malik A, Tandon N, et al. Tissue gene expression analysis using arrayed normalized cDNA libraries. Genome Res 2000; 10: 12301240.
  • 48
    Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, et al. A compendium of gene expression in normal human tissues. Physiol Genomics 2001; 7: 97104.
  • 49
    Chen G, Gharib TG, Huang CC, Taylor JM, Misek DE, Kardia SL, Giordano TJ, et al. Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics 2002; 1: 304313.
  • 50
    Essani NA, McGuire GM, Manning AM, Jaeschke H. Endotoxin-induced activation of the nuclear transcription factor kappa B and expression of E-selectin messenger RNA in hepatocytes, Kupffer cells, and endothelial cells in vivo. J Immunol 1996; 156: 29562963.