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Volumn 225, Issue 3, 2014, Pages 342-349

A statistical approach towards the derivation of predictive gene sets for potency ranking of chemicals in the mouse embryonic stem cell test

Author keywords

Concentration response analysis; Developmental toxicity; Embryonic stem cell test; Gene set; Phthalate monoesters; Potency ranking

Indexed keywords

BIOLOGICAL MARKER; PHTHALIC ACID; PHTHALIC ACID DERIVATIVE; TERATOGENIC AGENT;

EID: 84893489191     PISSN: 03784274     EISSN: 18793169     Source Type: Journal    
DOI: 10.1016/j.toxlet.2014.01.017     Document Type: Article
Times cited : (17)

References (47)
  • 1
    • 84875801161 scopus 로고    scopus 로고
    • Identification of stage-specific gene expression signatures in response to retinoic Acid during the neural differentiation of mouse embryonic stem cells
    • Akanuma H., Qin X.Y., Nagano R., Win-Shwe T.T., Imanishi S., Zaha H., Yoshinaga J., Fukuda T., Ohsako S., Sone H. Identification of stage-specific gene expression signatures in response to retinoic Acid during the neural differentiation of mouse embryonic stem cells. Front. Genet. 2012, 3:141.
    • (2012) Front. Genet. , vol.3 , pp. 141
    • Akanuma, H.1    Qin, X.Y.2    Nagano, R.3    Win-Shwe, T.T.4    Imanishi, S.5    Zaha, H.6    Yoshinaga, J.7    Fukuda, T.8    Ohsako, S.9    Sone, H.10
  • 2
    • 34447093802 scopus 로고    scopus 로고
    • In vitro immunotoxicity of bis(tri-n-butyltin)oxide (TBTO) studied by toxicogenomics
    • Baken K.A., Arkusz J., Pennings J.L., Vandebriel R.J., van Loveren H. In vitro immunotoxicity of bis(tri-n-butyltin)oxide (TBTO) studied by toxicogenomics. Toxicology 2007, 237:35-48.
    • (2007) Toxicology , vol.237 , pp. 35-48
    • Baken, K.A.1    Arkusz, J.2    Pennings, J.L.3    Vandebriel, R.J.4    van Loveren, H.5
  • 3
    • 79959310697 scopus 로고    scopus 로고
    • Toxicity testing in the 21 century: defining new risk assessment approaches based on perturbation of intracellular toxicity pathways
    • Bhattacharya S., Zhang Q., Carmichael P.L., Boekelheide K., Andersen M.E. Toxicity testing in the 21 century: defining new risk assessment approaches based on perturbation of intracellular toxicity pathways. PLoS One 2011, 6:e20887.
    • (2011) PLoS One , vol.6
    • Bhattacharya, S.1    Zhang, Q.2    Carmichael, P.L.3    Boekelheide, K.4    Andersen, M.E.5
  • 4
    • 0000343716 scopus 로고
    • Submodel Selection and Evaluation in Regression. The X-Random Case
    • Breiman L., SpectorF P. Submodel Selection and Evaluation in Regression. The X-Random Case. Int. Stat. Rev. 1992, 60.
    • (1992) Int. Stat. Rev. , pp. 60
    • Breiman, L.1    Spectorf, P.2
  • 5
    • 0027173483 scopus 로고
    • JunB differs from c-Jun in its DNA-binding and dimerization domains, and represses c-Jun by formation of inactive heterodimers
    • Deng T., Karin M. JunB differs from c-Jun in its DNA-binding and dimerization domains, and represses c-Jun by formation of inactive heterodimers. Genes Dev. 1993, 7:479-490.
    • (1993) Genes Dev. , vol.7 , pp. 479-490
    • Deng, T.1    Karin, M.2
  • 6
    • 36348960223 scopus 로고    scopus 로고
    • Prediction and classification of drug toxicity using probabilistic modeling of temporal metabolic data: the consortium on metabonomic toxicology screening approach
    • Ebbels T.M., Keun H.C., Beckonert O.P., Bollard M.E., Lindon J.C., Holmes E., Nicholson J.K. Prediction and classification of drug toxicity using probabilistic modeling of temporal metabolic data: the consortium on metabonomic toxicology screening approach. J. Proteome Res. 2007, 6:4407-4422.
    • (2007) J. Proteome Res. , vol.6 , pp. 4407-4422
    • Ebbels, T.M.1    Keun, H.C.2    Beckonert, O.P.3    Bollard, M.E.4    Lindon, J.C.5    Holmes, E.6    Nicholson, J.K.7
  • 8
    • 54349099534 scopus 로고    scopus 로고
    • Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies
    • Fetterman C.D., Rannala B., Walter M.A. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies. BMC Evol. Boil. 2008, 8:261.
    • (2008) BMC Evol. Boil. , vol.8 , pp. 261
    • Fetterman, C.D.1    Rannala, B.2    Walter, M.A.3
  • 10
    • 0036098620 scopus 로고    scopus 로고
    • The ECVAM international validation study on in vitro embryotoxicity tests: results of the definitive phase and evaluation of prediction models. European centre for the validation of alternative methods
    • Genschow E., Spielmann H., Scholz G., Seiler A., Brown N., Piersma A., Brady M., Clemann N., Huuskonen H., Paillard F., Bremer S., Becker K. The ECVAM international validation study on in vitro embryotoxicity tests: results of the definitive phase and evaluation of prediction models. European centre for the validation of alternative methods. Altern. Lab. Anim. 2002, 30:151-176.
    • (2002) Altern. Lab. Anim. , vol.30 , pp. 151-176
    • Genschow, E.1    Spielmann, H.2    Scholz, G.3    Seiler, A.4    Brown, N.5    Piersma, A.6    Brady, M.7    Clemann, N.8    Huuskonen, H.9    Paillard, F.10    Bremer, S.11    Becker, K.12
  • 11
    • 0027437399 scopus 로고
    • Development of an in vitro embryotoxicity test using murine embryonic stem cell cultures
    • Heuer J. Development of an in vitro embryotoxicity test using murine embryonic stem cell cultures. Toxicol. In Vitro 1993, 7:551-556.
    • (1993) Toxicol. In Vitro , vol.7 , pp. 551-556
    • Heuer, J.1
  • 12
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 13
    • 84864024007 scopus 로고    scopus 로고
    • Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with class III POU factors
    • Inoue F., Kurokawa D., Takahashi M., Aizawa S. Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with class III POU factors. Mol. Cell. Biol. 2012, 32:2618-2627.
    • (2012) Mol. Cell. Biol. , vol.32 , pp. 2618-2627
    • Inoue, F.1    Kurokawa, D.2    Takahashi, M.3    Aizawa, S.4
  • 14
    • 51749084417 scopus 로고    scopus 로고
    • Use of the rat postimplantation embryo culture to assess the embryotoxic potency within a chemical category and to identify toxic metabolites
    • Janer G.V.A, Gilsing H.D., Piersma A.H. Use of the rat postimplantation embryo culture to assess the embryotoxic potency within a chemical category and to identify toxic metabolites. Toxicol. In Vitro 2008, 22.
    • (2008) Toxicol. In Vitro , vol.22
    • Janer, G.V.A.1    Gilsing, H.D.2    Piersma, A.H.3
  • 15
    • 0019449053 scopus 로고
    • Effect of retinoic acid upon the chick embryonic morphogenetic systems I. The embryotoxicity dose range
    • Jelinek R., Kistler A. Effect of retinoic acid upon the chick embryonic morphogenetic systems I. The embryotoxicity dose range. Teratology 1981, 23:191-195.
    • (1981) Teratology , vol.23 , pp. 191-195
    • Jelinek, R.1    Kistler, A.2
  • 18
    • 2642595047 scopus 로고    scopus 로고
    • The roles of FGFs in the early development of vertebrate limbs
    • Martin G.R. The roles of FGFs in the early development of vertebrate limbs. Genes Dev. 1998, 12:1571-1586.
    • (1998) Genes Dev. , vol.12 , pp. 1571-1586
    • Martin, G.R.1
  • 21
    • 0026093209 scopus 로고
    • Isolation and characterization of a human cDNA encoding uracil-DNA glycosylase
    • Muller S.J., Caradonna S. Isolation and characterization of a human cDNA encoding uracil-DNA glycosylase. Biochim. Biophys. Acta 1991, 1088:197-207.
    • (1991) Biochim. Biophys. Acta , vol.1088 , pp. 197-207
    • Muller, S.J.1    Caradonna, S.2
  • 22
    • 0027509159 scopus 로고
    • Cell cycle regulation of a human cyclin-like gene encoding uracil-DNA glycosylase
    • Muller S.J., Caradonna S. Cell cycle regulation of a human cyclin-like gene encoding uracil-DNA glycosylase. J. Biol. Chem. 1993, 268:1310-1319.
    • (1993) J. Biol. Chem. , vol.268 , pp. 1310-1319
    • Muller, S.J.1    Caradonna, S.2
  • 23
    • 79955480444 scopus 로고    scopus 로고
    • Gene set assembly for quantitative prediction of developmental toxicity in the embryonic stem cell test
    • Pennings J.L., van Dartel D.A., Robinson J.F., Pronk T.E., Piersma A.H. Gene set assembly for quantitative prediction of developmental toxicity in the embryonic stem cell test. Toxicology 2011, 284:63-71.
    • (2011) Toxicology , vol.284 , pp. 63-71
    • Pennings, J.L.1    van Dartel, D.A.2    Robinson, J.F.3    Pronk, T.E.4    Piersma, A.H.5
  • 24
    • 79960847441 scopus 로고    scopus 로고
    • Comparison of MeHg-induced toxicogenomic responses across in vivo and in vitro models used in developmental toxicology
    • Robinson J.F., Theunissen P.T., van Dartel D.A., Pennings J.L., Faustman E.M., Piersma A.H. Comparison of MeHg-induced toxicogenomic responses across in vivo and in vitro models used in developmental toxicology. Reprod. Toxicol. 2011, 32:180-188.
    • (2011) Reprod. Toxicol. , vol.32 , pp. 180-188
    • Robinson, J.F.1    Theunissen, P.T.2    van Dartel, D.A.3    Pennings, J.L.4    Faustman, E.M.5    Piersma, A.H.6
  • 25
    • 84864572894 scopus 로고    scopus 로고
    • Cyclin-dependent kinase inhibitor p21(Waf1): contemporary view on its role in senescence and oncogenesis
    • Romanov V.S., Pospelov V.A., Pospelova T.V. Cyclin-dependent kinase inhibitor p21(Waf1): contemporary view on its role in senescence and oncogenesis. Biochem. Biokhim. 2012, 77:575-584.
    • (2012) Biochem. Biokhim. , vol.77 , pp. 575-584
    • Romanov, V.S.1    Pospelov, V.A.2    Pospelova, T.V.3
  • 26
    • 80053476385 scopus 로고    scopus 로고
    • Shortening and improving the embryonic stem cell test through the use of gene biomarkers of differentiation
    • Romero A.C., Vilanova E., Sogorb M.A. Shortening and improving the embryonic stem cell test through the use of gene biomarkers of differentiation. J. Toxicol. 2011, 286034.
    • (2011) J. Toxicol. , pp. 286034
    • Romero, A.C.1    Vilanova, E.2    Sogorb, M.A.3
  • 29
    • 84871921072 scopus 로고    scopus 로고
    • Dose response analysis of monophthalates in the murine embryonic stem cell test assessed by cardiomyocyte differentiation and gene expression
    • Schulpen S.H., Robinson J.F., Pennings J.L., van Dartel D.A., Piersma A.H. Dose response analysis of monophthalates in the murine embryonic stem cell test assessed by cardiomyocyte differentiation and gene expression. Reprod. Toxicol. 2012, 35:81-88.
    • (2012) Reprod. Toxicol. , vol.35 , pp. 81-88
    • Schulpen, S.H.1    Robinson, J.F.2    Pennings, J.L.3    van Dartel, D.A.4    Piersma, A.H.5
  • 30
    • 79959877538 scopus 로고    scopus 로고
    • The validated embryonic stem cell test to predict embryotoxicity in vitro
    • Seiler A.E., Spielmann H. The validated embryonic stem cell test to predict embryotoxicity in vitro. Nat. Protoc. 2014, 6:961-978.
    • (2014) Nat. Protoc. , vol.6 , pp. 961-978
    • Seiler, A.E.1    Spielmann, H.2
  • 31
    • 0036206395 scopus 로고    scopus 로고
    • Dose-response modeling of continuous endpoints
    • Slob W. Dose-response modeling of continuous endpoints. Toxicol. Sci.V 66 2002, 298-312.
    • (2002) Toxicol. Sci.V 66 , pp. 298-312
    • Slob, W.1
  • 32
    • 84858720808 scopus 로고    scopus 로고
    • Dimer-specific regulatory mechanisms within the NF-kappaB family of transcription factors
    • Smale S.T. Dimer-specific regulatory mechanisms within the NF-kappaB family of transcription factors. Immunol. Rev. 2012, 246:193-204.
    • (2012) Immunol. Rev. , vol.246 , pp. 193-204
    • Smale, S.T.1
  • 33
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: new features for data integration and network visualization
    • Smoot M.E., Ono K., Ruscheinski J., Wang P.L., Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27:431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 34
    • 84863852417 scopus 로고    scopus 로고
    • Compound-specific effects of diverse neurodevelopmental toxicants on global gene expression in the neural embryonic stem cell test (ESTn)
    • Theunissen P.T., Robinson J.F., Pennings J.L., van Herwijnen M.H., Kleinjans J.C., Piersma A.H. Compound-specific effects of diverse neurodevelopmental toxicants on global gene expression in the neural embryonic stem cell test (ESTn). Toxicol. Appl. Pharmacol. 2012, 262:330-340.
    • (2012) Toxicol. Appl. Pharmacol. , vol.262 , pp. 330-340
    • Theunissen, P.T.1    Robinson, J.F.2    Pennings, J.L.3    van Herwijnen, M.H.4    Kleinjans, J.C.5    Piersma, A.H.6
  • 35
    • 34548631764 scopus 로고    scopus 로고
    • SnapShot: forkhead transcription factors I
    • Tuteja G., Kaestner K.H. SnapShot: forkhead transcription factors I. Cell 2007, 130:1160.
    • (2007) Cell , vol.130 , pp. 1160
    • Tuteja, G.1    Kaestner, K.H.2
  • 39
    • 62549124073 scopus 로고    scopus 로고
    • Early gene expression changes during embryonic stem cell differentiation into cardiomyocytes and their modulation by monobutyl phthalate
    • van Dartel D.A., Pennings J.L., Hendriksen P.J., van Schooten F.J., Piersma A.H. Early gene expression changes during embryonic stem cell differentiation into cardiomyocytes and their modulation by monobutyl phthalate. Reprod. Toxicol. 2009, 27:93-102.
    • (2009) Reprod. Toxicol. , vol.27 , pp. 93-102
    • van Dartel, D.A.1    Pennings, J.L.2    Hendriksen, P.J.3    van Schooten, F.J.4    Piersma, A.H.5
  • 40
    • 79651475788 scopus 로고    scopus 로고
    • Discriminating classes of developmental toxicants using gene expression profiling in the embryonic stem cell test
    • van Dartel D.A., Pennings J.L., Robinson J.F., Kleinjans J.C., Piersma A.H. Discriminating classes of developmental toxicants using gene expression profiling in the embryonic stem cell test. Toxicol. Lett. 2011, 201:143-151.
    • (2011) Toxicol. Lett. , vol.201 , pp. 143-151
    • van Dartel, D.A.1    Pennings, J.L.2    Robinson, J.F.3    Kleinjans, J.C.4    Piersma, A.H.5
  • 41
    • 79960842777 scopus 로고    scopus 로고
    • The embryonic stem cell test combined with toxicogenomics as an alternative testing model for the assessment of developmental toxicity
    • van Dartel D.A., Piersma A.H. The embryonic stem cell test combined with toxicogenomics as an alternative testing model for the assessment of developmental toxicity. Reprod. Toxicol. 2011, 32:235-244.
    • (2011) Reprod. Toxicol. , vol.32 , pp. 235-244
    • van Dartel, D.A.1    Piersma, A.H.2
  • 42
    • 67650635159 scopus 로고    scopus 로고
    • Disentangling cellular proliferation and differentiation in the embryonic stem cell test, and its impact on the experimental protocol
    • van Dartel D.A., Zeijen N.J., de la Fonteyne L.J., van Schooten F.J., Piersma A.H. Disentangling cellular proliferation and differentiation in the embryonic stem cell test, and its impact on the experimental protocol. Reprod. Toxicol. 2009, 28:254-261.
    • (2009) Reprod. Toxicol. , vol.28 , pp. 254-261
    • van Dartel, D.A.1    Zeijen, N.J.2    de la Fonteyne, L.J.3    van Schooten, F.J.4    Piersma, A.H.5
  • 44
    • 84859976115 scopus 로고    scopus 로고
    • Transcriptomics analysis of primary mouse thymocytes exposed to bis(tri-n-butyltin)dioxide (TBTO)
    • van Kol S.W., Hendriksen P.J., van Loveren H., Peijnenburg A. Transcriptomics analysis of primary mouse thymocytes exposed to bis(tri-n-butyltin)dioxide (TBTO). Toxicology 2012, 296:37-47.
    • (2012) Toxicology , vol.296 , pp. 37-47
    • van Kol, S.W.1    Hendriksen, P.J.2    van Loveren, H.3    Peijnenburg, A.4
  • 45
    • 0025126386 scopus 로고
    • Jun: oncogene and transcription factor
    • Vogt P.K., Bos T.J. Jun: oncogene and transcription factor. Adv. Cancer Res. 1990, 55:1-35.
    • (1990) Adv. Cancer Res. , vol.55 , pp. 1-35
    • Vogt, P.K.1    Bos, T.J.2
  • 46
    • 84871963013 scopus 로고    scopus 로고
    • P21WAF1 and tumourigenesis: 20 years after
    • Warfel N.A., El-Deiry W.S. p21WAF1 and tumourigenesis: 20 years after. Curr. Opin. Oncol. 2013, 25:52-58.
    • (2013) Curr. Opin. Oncol. , vol.25 , pp. 52-58
    • Warfel, N.A.1    El-Deiry, W.S.2
  • 47
    • 73949116438 scopus 로고    scopus 로고
    • The mammalian anti-proliferative BTG/Tob protein family
    • Winkler G.S. The mammalian anti-proliferative BTG/Tob protein family. J. Cell Physiol. 2010, 222:66-72.
    • (2010) J. Cell Physiol. , vol.222 , pp. 66-72
    • Winkler, G.S.1


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