Cross-species comparative toxicogenomics as an aid to safety assessment

Expert Opinion on Drug Metabolism and Toxicology

Volumn 2, Issue 6, 2006, Pages 859-874

  Mattes, William B ^a,b  

^a Gene Logic Inc   (United States)

^b CRITICAL PATH INSTITUTE   (United States)

Author keywords

Cross species; Genomics; Orthologue; Safety assesment; Toxicogenomics

Indexed keywords

BACTERIUM LIPOPOLYSACCHARIDE; CIPROFIBRATE; ESTRADIOL; MESSENGER RNA; PARACETAMOL; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA AGONIST; PIRINIXIC ACID;

COMPARATIVE TOXICOLOGY; DATA BASE; DNA MICROARRAY; DNA SEQUENCE; DRUG OVERDOSE; EXPERIMENTAL DESIGN; FUNCTIONAL GENOMICS; GENE CONTROL; GENE MAPPING; GENETIC ALGORITHM; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; LIVER CARCINOGENESIS; LIVER CELL; LIVER NECROSIS; LIVER TOXICITY; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RISK ASSESSMENT; RNA SEQUENCE; SAFETY; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; TOXICOGENETICS; UNINDEXED SEQUENCE;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPECIES SPECIFICITY; TOXICITY TESTS; TOXICOGENETICS;

ANIMALIA;

EID: 33845503291     PISSN: 17425255     EISSN: None     Source Type: Journal    
DOI: 10.1517/17425255.2.6.859     Document Type: Review

References (127)

1. FERNIE KJ, SHUTT JL, MAYNE G et al.: Exposure to polybrominated diphenyl ethers (PBDEs): changes in thyroid, vitamin A, glutathione homeostasis, and oxidative stress in American kestrels (Falco sparverius). Toxicol. Sci. (2005) 88(2):375-383.
2. EATON D, KLAASSEN CD: Principles of Toxicology. In: Casarett and Doull's Toxicology. Klaassen CD (Ed.), McGraw-Hill, New York, USA (2001):11-34.
3. GALLO MA: History and Scope of Toxicology. In: Casarett and Doull's Toxicology. Klaassen CD (Ed.), McGraw-Hill, New York, USA (2001):3-10.
4. KLAASSEN CD: Nonmetallic Environmental Toxicants: Air Pollutants, Solvents and Vapors, and Pesticides. In: Gooman and Gilman's The Pharmacological Basis of Therapeutics. Gilman AG (Ed.), McGraw-Hill, New York, USA (1993):1615-1639.
5. STRACHAN ER, BENNETT A: Theobromine poisoning in dogs. Vet. Rec. (1994) 134(11):284.
6. VASSALLO JD, HICKS SM, DASTON GP, LEHMAN-MCKEEMAN LD: Metabolic detoxification determines species differences in coumarin-induced hepatotoxicity Toxicol. Sci. (2004) 80(2):249-257.
7. LIN JH, LU AY: Role of pharmacokinetics and metabolism in drug discovery and development. Pharmacol. Rev. (1997) 49(4):403-449.
8. NEBERT DW, ADESNIK M, COON MJ et al.: The P450 gene superfamily: recommended nomenclature. DNA (1987) 6(1):1-11.
9. FARR S, DUNN RT II: Concise review: gene expression applied to toxicology. Toxicol. Sci. (1999) 50(1):1-9.
10. KANEHISA M, GOTO S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. (2000) 28(1):27-30.
11. REECK GR, DE HAEN C, TELLER DC et al.: 'Homology' in proteins and nucleic acids: a terminology muddle and a way out of it. Cell (1987) 50(5):667.
12. DAYHOFF MO: Computer aids to protein sequence determination. J. Theor. Biol. (1965) 8(1):97-112.
13. NEEDLEMAN SB, WUNSCH CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. (1970) 48(3):443-453.
14. ALTSCHUL SF, GISH W, MILLER W, MYERS EW, LIPMAN DJ: Basic local alignment search tool. J. Mol. Biol. (1990) 215(3):403-410.
15. CORPET F: Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. (1988) 16(22):10881-10890.
16. HERSHKOVITZ MA, LEIPE DD: Phylogenetic Analysis. In: Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. Baxevanis AD, Ouellete BEF (Eds), Wiley-Liss, New York, USA (1988):189-230.
17. BRIFFEUIL P, BAUDOUX G, LAMBERT C et al.: Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions. Bioinformatics (1998) 14(4):357-366.
18. FITCH WM: Distinguishing homologous from analogous proteins. Syst. Zool. (1970) 19(2):99-113.
19. KOONIN EV, GALPERIN MY: Sequence - Evolution - Function: Computational Approaches in Comparative Genomics. Kluwer Academic Publishers, Norwell, MA, USA (2003).
20. CHEN F, MACKEY AJ, STOECKERT CJ Jr, ROOS DS: OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. (2006) 34(Database issue):D363-D368.
21. LI L, STOECKERT CJ Jr, ROOS DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. (2003) 13(9):2178-2189.
22. O'BRIEN KP, REMM M, SONNHAMMER EL: Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. (2005) 33(Database issue):D476-D480.
23. REMM M, STORM CE, SONNHAMMER EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. (2001) 314(5):1041-1052.
24. LEE Y, SULTANA R, PERTEA G et al.: Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res. (2002) 12(3):493-502.
25. WHEELER DL, BARRETT T, BENSON DA et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. (2006) 34(Database issue):D173-D180.
26. MATTES WB: Annotation and cross-indexing of array elements on multiple platforms. Environ. Health Perspect. (2004) 112(4):506-510.
27. DENNIS G Jr, SHERMAN BT, HOSACK DA et al.: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. (2003) 4(5):P3.
28. BOUTON CM, PEVSNER J: DRAGON: Database Referencing of Array Genes Online. Bioinformatics (2000) 16(11):1038-1039.
29. LIU G, LORAINE AE, SHIGETA R et al.: NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. (2003) 31(1):82-86.
30. ZHONG S, LI C. WONG WH: ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res. (2003) 31(13):3483-3486.
31. BLUTHGEN N, KIELBASA SM, CAJAVEC B, HERZEL H: HOMGL-comparing genelists across species and with different accession numbers. Bioinformatics (2004) 20(1):125-126.
32. CHEUNG KH, HAGER J, PAN D et al.: KARMA: a web server application for comparing and annotating heterogeneous microarray platforms. Nucleic Acids Res. (2004) 32(Web Server issue):W441-W444.
33. TSAI J, SULTANA R, LEE Y et al.: RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol. (2001) 2(11):SOFTWARE0002.
34. BURGOON LD, BOUTROS PC, DERE E, ZACHAREWSKI TR: dbZach: a MIAME-compliant toxicogenomic supportive relational database. Toxicol. Sci. (2006) 90(2):558-568.
35. WALKER SJ, WANG Y, GRANT KA, CHAN F, HELLMANN GM: Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates. J. Neurosci. Methods (2006) 152(1-2):179-189.
36. JI W, ZHOU W, GREGG K, YU N, DAVIS S: A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res. (2004) 32(11):e93.
37. VERDUGO RA, MEDRANO JF: Comparison of gene coverage of mouse oligonucleotide microarray platforms. BMC Genomics (2006) 7:58.
38. HEWITT NJ, BUHRING KU, DASENBROCK J et al.: Studies comparing in vivo: in vitro metabolism of three pharmaceutical compounds in rat, dog, monkey, and human using cryopreserved hepatocytes, microsomes, and collagen gel immobilized hepatocyte cultures. Drug Metab. Dispos. (2001) 29(7):1042-1050.
39. AMMERSCHLAEGER M, BEIGEL J, KLEIN KU, MUELLER SO: Characterization of the species-specificity of peroxisome proliferators in rat and human hepatocytes. Toxicol. Sci. (2004) 78(2):229-240.
40. LAWRENCE JW, LI Y, CHEN S et al.: Differential gene regulation in human versus rodent hepatocytes by peroxisome proliferator-activated receptor (PPAR) alpha. PPAR alpha fails to induce peroxisome proliferation-associated genes in human cells independently of the level of receptor expresson. J. Biol. Chem. (2001) 276(34):31521-31527.
41. BUTTE A: The use and analysis of microarray data. Nat. Rev. Drug Discov. (2002) 1(12):951-960.
42. RINGNER M, PETERSON C, KHAN J: Analyzing array data using supervised methods. Pharmacogenomics (2002) 3(3):403-415.
43. REINER A, YEKUTIELI D, BENJAMINI Y: Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics (2003) 19(3):368-375.
44. IMBEAUD S, AUFFRAY C: 'The 39 steps' in gene expression profiling: critical issues and proposed best practices for microarray experiments. Drug Discov. Today (2005) 10(17):1175-1182.
45. SHEDDEN K, CHEN W, KUICK R et al.: Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data. BMC Bioinformatics (2005) 6:26.
46. ALLISON DB, CUI X, PAGE GP, SABRIPOUR M: Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet. (2006) 7(1):55-65.
47. JI H, DAVIS RW: Data quality in genomics and microarrays. Nat. Biotechnol. (2006) 24(9):1112-1113.
48. KHATRI P, DRAGHICI S: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics (2005) 21(18):3587-3595.
49. HE YD, DAI H, SCHADT EE et al.: Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics (2003) 19(8):956-965.
50. CHOE SE, BOUTROS M, MICHELSON AM, CHURCH GM, HALFON MS: Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol. (2005) 6(2):R16.
51. CURRIE RA, ORPHANIDES G, MOGGS JG: Mapping molecular responses to xenoestrogens through Gene Ontology and pathway analysis of toxicogenomic data. Reprod. Toxicol. (2005) 20(3):433-440.
52. CURRIE RA, BOMBAIL V, OLIVER JD et al.: Gene ontology mapping as an unbiased method for identifying molecular pathways and processes affected by toxicant exposure: application to acute effects caused by the rodent non-genotoxic carcinogen diethylhexylphthalate. Toxicol. Sci. (2005) 86(2):453-469.
53. CAMON E, MAGRANE M, BARRELL D et al.: The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res. (2003) 13(4):662-672.
54. ALLOCCO DJ, KOHANE IS, BUTTE AJ: Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics (2004) 5(1):18.
55. WEBER LW, BOLL M, STAMPFL A: Maintaining cholesterol homeostasis: sterol regulatory element-binding proteins. World J. Gastroenterol. (2004) 10(21):3081-3087.
56. BERRY MD: Glyceraldehyde-3-phosphate dehydrogenase as a target for small-molecule disease-modifying therapies in human neurodegenerative disorders. J. Psychiatry Neurosci. (2004) 29(5):337-345.
57. BHAT R, BRESNICK E: Glycine N-methyltransferase is an example of functional diversity. Role as a polycyclic aromatic hydrocarbon-binding receptor. J. Biol. Chem. (1997) 272(34):21221-21226.
58. CHUANG DM, HOUGH C, SENATOROV VV: Glyceraldehyde-3-phosphate dehydrogenase, apoptosis, and neurodegenerative diseases. Ann. Rev. Pharmacol. Toxicol. (2005) 45:269-290.
59. HIRANO K, MIKI Y, HIRAI Y et al.: A multifunctional shuttling protein nucleolin is a macrophage receptor for apoptotic cells. J. Biol. Chem. (2005) 280(47):39284-39293.
60. HAFT DH, SELENGUT JD, BRINKAC LM, ZAFAR N, WHITE O: Genome properties: a system for the investigation of prokaryotic genetic content for microbiology genome annotation and comparative genomics. Bioinformatics (2005) 21(3):293-306.
61. OVERBEEK R, FONSTEIN M, D'SOUZA M, PUSCH GD, MALTSEV N: The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA (1999) 96(6):2896-2901.
62. DUBCHAK I, BRUDNO M, LOOTS GG et al.: Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. (2000) 10(9):1304-1306.
63. FRAZER KA, PACHTER L, POLIAKOV A, RUBIN EM, DUBCHAK I: VISTA: computational tools for comparative genomics. Nucleic Acids Res. (2004) 32(Web Server issue):W273-W279.
64. ZAVOLAN M, VAN NIMWEGEN E, GAASTERLAND T: Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res. (2002) 12(9):1377-1385.
65. XU Q, MODREK B, LEE C: Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res. (2002) 30(17):3754-3766.
66. KAN Z, GARRETT-ENGELE PW, JOHNSON JM, CASTLE JC: Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles. Nucleic Acids Res. (2005) 33(17):5659-5666.
67. THANARAJ TA, CLARK F, MUILU J: Conservation of human alternative splice events in mouse. Nucleic Acids Res. (2003) 31(10):2544-2552.
68. MAKALOWSKI W, ZHANG J, BOGUSKI MS: Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome. Res. (1996) 6(9):846-857.
69. MAKALOWSKI W, BOGUSKI MS: Evolutionary parameters of the transcribed mammalian genome: an analysis of 2820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. USA (1998) 95(16):9407-9412.
70. KOLBE D, TAYLOR J, ELNITSKI L et al.: Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res. (2004) 14(4):700-707.
71. LEE S, KOHANE I, KASIF S: Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics (2005) 6:168.
72. FRAZER KA, ELNITSKI L, CHURCH DM, DUBCHAK I, HARDISON RC: Cross-species sequence comparisons: a review of methods and available resources. Genome Res. (2003) 13(1):1-12.
73. REED JC, DOCTOR KS, GODZIK A: The domains of apoptosis: a genomics perspective. Sci. STKE (2004) 2004(239):re9.
74. ARAVIND L, DIXIT VM, KOONIN EV: Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons. Science (2001) 291(5507):1279-1284.
75. HAHN ME, KARCHNER SI, SHAPIRO MA, PERERA SA: Molecular evolution of two vertebrate aryl hydrocarbon (dioxin) receptors (AHR1 and AHR2) and the PAS family. Proc. Natl. Acad. Sci. USA (1997) 94(25):13743-13748.
76. THOMAS RS, PENN SG, HOLDEN K, BRADFIELD CA, RANK DR: Sequence variation and phylogenetic history of the mouse Ahr gene. Pharmacogenetics (2002) 12(2):151-163.
77. LECLUYSE EL: Pregnane X receptor: molecular basis for species differences in CYP3A induction by xenobiotics. Chem. Biol. Interact. (2001) 134(3):283-289.
78. KIM HJ, KIM JY, PARK SK et al.: Differential regulation of human and mouse orphan nuclear receptor small heterodimer partner promoter by sterol regulatory element binding protein-1. J. Biol. Chem. (2004) 279(27):28122-28131.
79. KRASOWSKI MD, YASUDA K, HAGEY LR, SCHUETZ EG: Evolutionary selection across the nuclear hormone receptor superfamily with a focus on the NR1I subfamily (vitamin D, pregnane X, and constitutive androstane receptors). Nucl. Recept. (2005) 3:2.
80. ZHANG Z, BURCH PE, COONEY AJ et al.: Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome. Genome Res. (2004) 14(4):580-590.
81. MAITINGLY CJ, COLBY GT, FORREST JN, BOYER JL: The Comparative Toxicogenomics Database (CTD). Environ. Health Perspect. (2003) 111(6):793-795.
82. JAMES LP, MAYEUX PR, HINSON JA: Acetaminophen-induced hepatotoxicity. Drug Metab. Dispos. (2003) 31(12):1499-1506.
83. RUEPP SU, TONGE RP, SHAW J, WALLIS N, POGNAN F: Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol. Sci. (2002) 65(1):135-150.
84. REILLY TP, BOURDI M, BRADY JN et al.: Expression profiling of acetaminophen liver toxicity in mice using microarray technology. Biochem. Biophys. Res. Commun. (2001) 282(1):321-328.
85. WILLIAMS DP, GARCIA-ALLAN C, HANTON G et al.: Time course toxicogenomic profiles in CD-1 mice after nontoxic and nonlethal hepatotoxic paracetamol administration. Chem. Res. Toxicol. (2004) 17(12):1551-1561.
86. HEINLOTH AN, IRWIN RD, BOORMAN GA et al.: Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol. Sci. (2004) 80(1):193-202.
87. HUANG Q, JIN X, GAILLARD ET et al.: Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants. Mutat. Res. (2004) 549(1-2):147-167.
88. MINAMI K, SAITO T, NARAHARA M et al.: Relationship between hepatic gene expression profiles and hepatotoxicity in five typical hepatotoxicant-administered rats. Toxicol. Sci. (2005) 87(1):296-305.
89. HARRIS AJ, DIAL SL, CASCIANO DA: Comparison of basal gene expression profiles and effects of hepatocarcinogens on gene expression in cultured primary human hepatocytes and HepG2 cells. Mutat. Res. (2004) 549(1-2):79-99.
90. LYOUMI S, PUY H, TAMION F et al.: Heme and acute inflammation role in vivo of heme in the hepatic expression of positive acute-phase reactants in rats. Eur. J. Biochem. (1999) 261(1):190-196.
91. LUYENDYK JP, MATTES WB, BURGOON LD et al.: Gene expression analysis points to hemostasis in livers of rats cotreated with lipopolysaccharide and ranitidine. Toxicol. Sci. (2004) 80(1):203-213.
92. BULERA SJ, EDDY SM, FERGUSON E et al.: RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. Hepatology (2001) 33(5):1239-1258.
93. VASSEUR S, HOFFMEISTER A, GARCIA-MONTERO A et al.: Mice with targeted disruption of p8 gene show increased sensitivity to lipopolysaccharide and DNA microarray analysis of livers reveals an aberrant gene expression response. BMC Gastroenterol. (2003) 3:25.
94. HIGGINS MA, BERRIDGE BR, MILLS BJ et al.: Gene expression analysis of the acute phase response using a canine microarray. Toxicol. Sci. (2003) 74(2):470-484.
95. LIU S, GALLO DJ, GREEN AM et al.: Role of toll-like receptors in changes in gene expression and NF-kappa B activation in mouse hepatocytes stimulated with lipopolysaccharide. Infect. Immun. (2002) 70(7):3433-3442.
96. VANDEN HEUVEL JP: Peroxisome proliferator-activated receptors: a critical link among fatty acids, gene expression and carcinogenesis. J. Nutr. (1999) 129(2S Suppl.):575S-580S.
97. HOLDEN PR, TUGWOOD JD: Peroxisome proliferator-activated receptor alpha: role in rodent liver cancer and species differences. J. Mol. Endocrinol. (1999) 22(1):1-8.
98. BOITIER E, GAUTIER JC, ROBERTS R: Advances in understanding the regulation of apoptosis and mitosis by peroxisome-proliferator activated receptors in pre-clinical models: relevance for human health and disease. Comp. Hepatol. (2003) 2(1):3.
99. KLAUNIG JE, BABICH MA, BAETCKE KP et al.: PPARalpha agonist-induced rodent tumors: modes of action and human relevance. Crit. Rev. Toxicol. (2003) 33(6):655-780.
100. ANDERSON SP, HOWROYD P, LIU J et al.: The transcriptional response to a peroxisome proliferator-activated receptor alpha agonist includes increased expression of proteome maintenance genes. J. Biol. Chem. (2004) 279(50):52390-52398.
101. YAMAZAKI K, KUROMITSU J, TANAKA I: Microarray analysis of gene expression changes in mouse liver induced by peroxisome proliferator-activated receptor alpha agonists. Biochem. Biophys. Res. Commun. (2002) 290(3):1114-1122.
102. CHERKAOUI-MALKI M, MEYER K, CAO WQ et al.: Identification of novel peroxisome proliferator-activated receptor alpha (PPARalpha) target genes in mouse liver using cDNA microarray analysis. Gene Expr. (2001) 9(6):291-304.
103. KERSTEN S, MANDARD S, ESCHER P et al.: The peroxisome proliferator-activated receptor alpha regulates amino acid metabolism. FASEB J. (2001) 15(11):1971-1978.
104. BAKER VA, HARRIES HM, WARING JF et al.: Clofibrate-induced gene expression changes in rat liver: a cross-laboratory analysis using membrane cDNA arrays. Environ. Health Perspect. (2004) 112(4):428-438.
105. HAMADEH HK, BUSHEL PR, JAYADEV S et al.: Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci. (2002) 67(2):219-231.
106. JUNG JW, PARK JS, HWANG JW et al.: Gene expression analysis of peroxisome proliferators- and phenytoin-induced hepatotoxicity using cDNA microarray. J. Vet. Med. Sci. (2004) 66(11):1329-1333.
107. MICHEL C, DESDOUETS C, SACRE-SALEM B et al.: Liver gene expression profiles of rats treated with clofibric acid: comparison of whole liver and laser capture microdissected liver. Am. J. Pathol. (2003) 163(6):2191-2199.
108. ULRICH RG, ROCKETT JC, GIBSON GG, PETTIT SD: Overview of an interlaboratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. Environ. Health Perspect. (2004) 112(4):423-427.
109. KRAMER JA, BLOMME EA, BUNCH RT et al.: Transcription profiling distinguishes dose-dependent effects in the livers of rats treated with clofibrate. Toxicol. Pathol. (2003) 31(4):417-431.
110. YADETIE F, LAEGREID A, BAKKE I et al.: Liver gene expression in rats in response to the peroxisome proliferator-activated receptor-alpha agonist ciprofibrate. Physiol. Genomics (2003) 15(1):9-19.
111. CARIELLO NF, ROMACH EH, COLTON HM et al.: Gene expression profiling of the PPAR-alpha agonist ciprofibrate in the cynomolgus monkey liver. Toxicol. Sci. (2005) 88(1):250-264.
112. RICHERT L, LAMBOLEY C, VIOLLON-ABADIE C et al.: Effects of clofibric acid on mRNA expression profiles in primary cultures of rat, mouse and human hepatocytes. Toxicol. Appl. Pharmacol. (2003) 191(2):130-146.
113. SAFE SH, PALLARONI L, YOON K et al.: Problems for risk assessment of endocrine-active estrogenic compounds. Environ. Health Perspect. (2002) 110(Suppl. 6):925-929.
114. 2+ fluxes and prolactin release in GH3/B6 pituitary tumor cells. Environ. Health Perspect. (2005) 113(4):431-439.
115. KATO N, SHIBUTANI M, TAKAGI H et al.: Gene expression profile in the livers of rats orally administered ethinylestradiol for 28 days using a microarray technique. Toxicology (2004) 200(2-3):179-192.
116. STAHLBERG N, MERINO R, HERNANDEZ LH et al.: Exploring hepatic hormone actions using a compilation of gene expression profiles. BMC Physiol. (2005) 5(1):8.
117. NACIFF JM, HESS KA, OVERMANN GJ et al.: Gene expression changes induced in the testis by transplacental exposure to high and low doses of 17[alpha]-ethynyl estradiol, genistein, or bisphenol A. Toxicol. Sci. (2005) 86(2):396-416.
118. ROCKETT JC, KAVLOCK RJ, LAMBRIGHT CR et al.: DNA arrays to monitor gene expression in rat blood and uterus following 17beta-estradiol exposure: biomonitoring environmental effects using surrogate tissues. Toxicol. Sci. (2002) 69(1):49-59.
119. FERTUCK KC, ECKEL JE, GENNINGS C, ZACHAREWSKI TR: Identification of temporal patterns of gene expression in the uteri of immature, ovariectomized mice following exposure to ethynylestradiol. Physiol. Genomics (2003) 15(2):127-141.
120. KWEKEL JC, BURGOON LD, BURT JW, HARKEMA JR, ZACHAREWSKI TR: A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling. Physiol. Genomics (2005) 23(3):327-342.
121. TATUSOVA TA, MADDEN TL: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. (1999) 174(2):247-250.
122. AARON CS, BOLCSFOLDI G, GLATT HR et al.: Mammalian cell gene mutation assays working group report. Mutat. Res. (1994) 312(3):235-239.
123. BAKER TK, CARFAGNA MA, GAO H et al.: Temporal gene expression analysis of monolayer cultured rat hepatocytes. Chem. Res. Toxicol. (2001) 14(9):1218-1231.
124. WARING JF, CIURLIONIS R, JOLLY RA et al.: Isolated human hepatocytes in culture display markedly different gene expression patterns depending on attachment status. Toxicol. In Vitro (2003) 17(5-6):693-701.
125. MOTTAGUI-TABAR S, FAGHIHI MA, MIZUNO Y et al.: Identification of functional SNPs in the 5-prime flanking sequences of human genes. BMC Genomics (2005) 6(1):18.
126. GURYEV V, BEREZIKOV E, CUPPEN E: CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences. BMC Genomics (2005) 6(1):10.
127. FREIMUTH RR, STORMO GD, MCLEOD HL: PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis. Hum. Mutat. (2005) 25(2):110-117.