메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: Transcriptional dynamics and regulatory structures

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE ANALYSIS; COMPUTATIONAL APPROACH; HETEROGENEOUS SOURCES; REGULATORY MECHANISM; REGULATORY STRUCTURE; TRANSCRIPTIONAL CONTROL; TRANSCRIPTIONAL MODULES; TRANSCRIPTIONAL REGULATOR;

EID: 77957778177     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-515     Document Type: Article
Times cited : (17)

References (85)
  • 1
    • 26844433194 scopus 로고    scopus 로고
    • Antiinflammatory action of glucocorticoids--new mechanisms for old drugs
    • 10.1056/NEJMra050541, 16236742
    • Rhen T, Cidlowski JA. Antiinflammatory action of glucocorticoids--new mechanisms for old drugs. N Engl J Med 2005, 353(16):1711-1723. 10.1056/NEJMra050541, 16236742.
    • (2005) N Engl J Med , vol.353 , Issue.16 , pp. 1711-1723
    • Rhen, T.1    Cidlowski, J.A.2
  • 2
    • 31944440761 scopus 로고    scopus 로고
    • Corticosteroid effects on cell signalling
    • 10.1183/09031936.06.00125404, 16452600
    • Barnes PJ. Corticosteroid effects on cell signalling. Eur Respir J 2006, 27(2):413-426. 10.1183/09031936.06.00125404, 16452600.
    • (2006) Eur Respir J , vol.27 , Issue.2 , pp. 413-426
    • Barnes, P.J.1
  • 3
    • 0033629479 scopus 로고    scopus 로고
    • Advances in glucocorticoid therapy
    • Baxter JD. Advances in glucocorticoid therapy. Adv Intern Med 2000, 45:317-349.
    • (2000) Adv Intern Med , vol.45 , pp. 317-349
    • Baxter, J.D.1
  • 5
    • 0030426743 scopus 로고    scopus 로고
    • An overview of the adverse reactions to adrenal corticosteroids
    • Frauman AG. An overview of the adverse reactions to adrenal corticosteroids. Adverse Drug React Toxicol Rev 1996, 15(4):203-206.
    • (1996) Adverse Drug React Toxicol Rev , vol.15 , Issue.4 , pp. 203-206
    • Frauman, A.G.1
  • 6
    • 0036810356 scopus 로고    scopus 로고
    • Mechanisms involved in the side effects of glucocorticoids
    • 10.1016/S0163-7258(02)00297-8, 12441176
    • Schacke H, Docke WD, Asadullah K. Mechanisms involved in the side effects of glucocorticoids. Pharmacol Ther 2002, 96(1):23-43. 10.1016/S0163-7258(02)00297-8, 12441176.
    • (2002) Pharmacol Ther , vol.96 , Issue.1 , pp. 23-43
    • Schacke, H.1    Docke, W.D.2    Asadullah, K.3
  • 7
    • 0029788874 scopus 로고    scopus 로고
    • Dyslipidaemia and hyperlipidaemia following renal transplantation
    • 10.1007/BF02550506, 8899484
    • Locsey L, Asztalos L, Kincses Z, Gyorfi F, Berczi C. Dyslipidaemia and hyperlipidaemia following renal transplantation. Int Urol Nephrol 1996, 28(3):419-430. 10.1007/BF02550506, 8899484.
    • (1996) Int Urol Nephrol , vol.28 , Issue.3 , pp. 419-430
    • Locsey, L.1    Asztalos, L.2    Kincses, Z.3    Gyorfi, F.4    Berczi, C.5
  • 8
    • 27144451563 scopus 로고    scopus 로고
    • Pharmacogenomic responses of rat liver to methylprednisolone: an approach to mining a rich microarray time series
    • 10.1208/aapsj070117, 2607485,2607485, 16146338
    • Almon RR, Dubois DC, Jin JY, Jusko WJ. Pharmacogenomic responses of rat liver to methylprednisolone: an approach to mining a rich microarray time series. Aaps J 2005, 7(1):E156-194. 10.1208/aapsj070117, 2607485,2607485, 16146338.
    • (2005) Aaps J , vol.7 , Issue.1
    • Almon, R.R.1    Dubois, D.C.2    Jin, J.Y.3    Jusko, W.J.4
  • 9
    • 3543069887 scopus 로고    scopus 로고
    • The genomic response of skeletal muscle to methylprednisolone using microarrays: tailoring data mining to the structure of the pharmacogenomic time series
    • 10.1517/14622416.5.5.525, 2607486, 15212590
    • Almon RR, DuBois DC, Piel WH, Jusko WJ. The genomic response of skeletal muscle to methylprednisolone using microarrays: tailoring data mining to the structure of the pharmacogenomic time series. Pharmacogenomics 2004, 5(5):525-552. 10.1517/14622416.5.5.525, 2607486, 15212590.
    • (2004) Pharmacogenomics , vol.5 , Issue.5 , pp. 525-552
    • Almon, R.R.1    DuBois, D.C.2    Piel, W.H.3    Jusko, W.J.4
  • 10
    • 27144458368 scopus 로고    scopus 로고
    • Corticosteroid-regulated genes in rat kidney: mining time series array data
    • 10.1152/ajpendo.00196.2005, 15985454
    • Almon RR, Lai W, DuBois DC, Jusko WJ. Corticosteroid-regulated genes in rat kidney: mining time series array data. Am J Physiol Endocrinol Metab 2005, 289(5):E870-882. 10.1152/ajpendo.00196.2005, 15985454.
    • (2005) Am J Physiol Endocrinol Metab , vol.289 , Issue.5
    • Almon, R.R.1    Lai, W.2    DuBois, D.C.3    Jusko, W.J.4
  • 11
    • 34249785105 scopus 로고    scopus 로고
    • A microarray analysis of the temporal response of liver to methylprednisolone: a comparative analysis of two dosing regimens
    • 10.1210/en.2006-0790, 17303664
    • Almon RR, DuBois DC, Jusko WJ. A microarray analysis of the temporal response of liver to methylprednisolone: a comparative analysis of two dosing regimens. Endocrinology 2007, 148(5):2209-2225. 10.1210/en.2006-0790, 17303664.
    • (2007) Endocrinology , vol.148 , Issue.5 , pp. 2209-2225
    • Almon, R.R.1    DuBois, D.C.2    Jusko, W.J.3
  • 12
    • 34548071748 scopus 로고    scopus 로고
    • Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens
    • 10.1152/physiolgenomics.00242.2006, 17473217
    • Almon RR, DuBois DC, Yao Z, Hoffman EP, Ghimbovschi S, Jusko WJ. Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens. Physiol Genomics 2007, 30(3):282-299. 10.1152/physiolgenomics.00242.2006, 17473217.
    • (2007) Physiol Genomics , vol.30 , Issue.3 , pp. 282-299
    • Almon, R.R.1    DuBois, D.C.2    Yao, Z.3    Hoffman, E.P.4    Ghimbovschi, S.5    Jusko, W.J.6
  • 13
    • 42549101936 scopus 로고    scopus 로고
    • Mathematical modeling of corticosteroid pharmacogenomics in rat muscle following acute and chronic methylprednisolone dosing
    • 10.1021/mp700094s, 18271548
    • Yao Z, Hoffman EP, Ghimbovschi S, Dubois DC, Almon RR, Jusko WJ. Mathematical modeling of corticosteroid pharmacogenomics in rat muscle following acute and chronic methylprednisolone dosing. Mol Pharm 2008, 5(2):328-339. 10.1021/mp700094s, 18271548.
    • (2008) Mol Pharm , vol.5 , Issue.2 , pp. 328-339
    • Yao, Z.1    Hoffman, E.P.2    Ghimbovschi, S.3    Dubois, D.C.4    Almon, R.R.5    Jusko, W.J.6
  • 14
    • 0036139446 scopus 로고    scopus 로고
    • Pharmacodynamics and pharmacogenomics of methylprednisolone during 7-day infusions in rats
    • 10.1124/jpet.300.1.245, 11752123
    • Ramakrishnan R, DuBois DC, Almon RR, Pyszczynski NA, Jusko WJ. Pharmacodynamics and pharmacogenomics of methylprednisolone during 7-day infusions in rats. J Pharmacol Exp Ther 2002, 300(1):245-256. 10.1124/jpet.300.1.245, 11752123.
    • (2002) J Pharmacol Exp Ther , vol.300 , Issue.1 , pp. 245-256
    • Ramakrishnan, R.1    DuBois, D.C.2    Almon, R.R.3    Pyszczynski, N.A.4    Jusko, W.J.5
  • 15
    • 0032456263 scopus 로고    scopus 로고
    • Fourth-generation model for corticosteroid pharmacodynamics: a model for methylprednisolone effects on receptor/gene-mediated glucocorticoid receptor down-regulation and tyrosine aminotransferase induction in rat liver
    • Sun YN, DuBois DC, Almon RR, Jusko WJ. Fourth-generation model for corticosteroid pharmacodynamics: a model for methylprednisolone effects on receptor/gene-mediated glucocorticoid receptor down-regulation and tyrosine aminotransferase induction in rat liver. J Pharmacokinet Biopharm 1998, 26(3):289-317.
    • (1998) J Pharmacokinet Biopharm , vol.26 , Issue.3 , pp. 289-317
    • Sun, Y.N.1    DuBois, D.C.2    Almon, R.R.3    Jusko, W.J.4
  • 16
    • 0024204439 scopus 로고
    • Regulation of glucocorticoid receptor expression: evidence for transcriptional and posttranslational mechanisms
    • 10.1210/mend-2-12-1256, 3216865
    • Dong Y, Poellinger L, Gustafsson JA, Okret S. Regulation of glucocorticoid receptor expression: evidence for transcriptional and posttranslational mechanisms. Mol Endocrinol 1988, 2(12):1256-1264. 10.1210/mend-2-12-1256, 3216865.
    • (1988) Mol Endocrinol , vol.2 , Issue.12 , pp. 1256-1264
    • Dong, Y.1    Poellinger, L.2    Gustafsson, J.A.3    Okret, S.4
  • 17
    • 0027266849 scopus 로고
    • Homologous down regulation of the glucocorticoid receptor: the molecular machinery
    • Oakley RH, Cidlowski JA. Homologous down regulation of the glucocorticoid receptor: the molecular machinery. Crit Rev Eukaryot Gene Expr 1993, 3(2):63-88.
    • (1993) Crit Rev Eukaryot Gene Expr , vol.3 , Issue.2 , pp. 63-88
    • Oakley, R.H.1    Cidlowski, J.A.2
  • 18
    • 0024553710 scopus 로고
    • Regulation of glucocorticoid receptor protein and mRNA levels
    • Vedeckis WV, Ali M, Allen HR. Regulation of glucocorticoid receptor protein and mRNA levels. Cancer Res 1989, 49(8):2295s-2302s.
    • (1989) Cancer Res , vol.49 , Issue.8
    • Vedeckis, W.V.1    Ali, M.2    Allen, H.R.3
  • 19
    • 0036553438 scopus 로고    scopus 로고
    • Pharmacodynamics and pharmacogenomics of diverse receptor-mediated effects of methylprednisolone in rats using microarray analysis
    • 10.1023/A:1019762323576, 12361239
    • Almon RR, DuBois DC, Brandenburg EH, Shi W, Zhang S, Straubinger RM, Jusko WJ. Pharmacodynamics and pharmacogenomics of diverse receptor-mediated effects of methylprednisolone in rats using microarray analysis. J Pharmacokinet Pharmacodyn 2002, 29(2):103-129. 10.1023/A:1019762323576, 12361239.
    • (2002) J Pharmacokinet Pharmacodyn , vol.29 , Issue.2 , pp. 103-129
    • Almon, R.R.1    DuBois, D.C.2    Brandenburg, E.H.3    Shi, W.4    Zhang, S.5    Straubinger, R.M.6    Jusko, W.J.7
  • 20
    • 0032449041 scopus 로고    scopus 로고
    • Dose-dependence and repeated-dose studies for receptor/gene-mediated pharmacodynamics of methylprednisolone on glucocorticoid receptor down-regulation and tyrosine aminotransferase induction in rat liver
    • 10.1023/A:1020746822634, 10485078
    • Sun YN, DuBois DC, Almon RR, Pyszczynski NA, Jusko WJ. Dose-dependence and repeated-dose studies for receptor/gene-mediated pharmacodynamics of methylprednisolone on glucocorticoid receptor down-regulation and tyrosine aminotransferase induction in rat liver. J Pharmacokinet Biopharm 1998, 26(6):619-648. 10.1023/A:1020746822634, 10485078.
    • (1998) J Pharmacokinet Biopharm , vol.26 , Issue.6 , pp. 619-648
    • Sun, Y.N.1    DuBois, D.C.2    Almon, R.R.3    Pyszczynski, N.A.4    Jusko, W.J.5
  • 21
    • 0032695544 scopus 로고    scopus 로고
    • Glucocorticoid regulation of inflammation: the plot thickens
    • 10.1007/s000110050503, 10598010
    • Morand EF, Leech M. Glucocorticoid regulation of inflammation: the plot thickens. Inflamm Res 1999, 48(11):557-560. 10.1007/s000110050503, 10598010.
    • (1999) Inflamm Res , vol.48 , Issue.11 , pp. 557-560
    • Morand, E.F.1    Leech, M.2
  • 22
    • 0032936343 scopus 로고    scopus 로고
    • Glucocorticoids and insulin resistance: old hormones, new targets
    • 10.1042/CS19980388, 10209084
    • Andrews RC, Walker BR. Glucocorticoids and insulin resistance: old hormones, new targets. Clin Sci (Lond) 1999, 96(5):513-523. 10.1042/CS19980388, 10209084.
    • (1999) Clin Sci (Lond) , vol.96 , Issue.5 , pp. 513-523
    • Andrews, R.C.1    Walker, B.R.2
  • 23
    • 0141742369 scopus 로고    scopus 로고
    • Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays
    • 10.1124/jpet.103.053256, 12808002
    • Jin JY, Almon RR, DuBois DC, Jusko WJ. Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays. J Pharmacol Exp Ther 2003, 307(1):93-109. 10.1124/jpet.103.053256, 12808002.
    • (2003) J Pharmacol Exp Ther , vol.307 , Issue.1 , pp. 93-109
    • Jin, J.Y.1    Almon, R.R.2    DuBois, D.C.3    Jusko, W.J.4
  • 24
    • 3543068702 scopus 로고    scopus 로고
    • Microarray platforms--comparisons and contrasts
    • 10.1517/14622416.5.5.487, 15212585
    • Hardiman G. Microarray platforms--comparisons and contrasts. Pharmacogenomics 2004, 5(5):487-502. 10.1517/14622416.5.5.487, 15212585.
    • (2004) Pharmacogenomics , vol.5 , Issue.5 , pp. 487-502
    • Hardiman, G.1
  • 25
    • 2642561079 scopus 로고    scopus 로고
    • Are data from different gene expression microarray platforms comparable?
    • 10.1016/j.ygeno.2004.01.004, 15177569
    • Jarvinen AK, Hautaniemi S, Edgren H, Auvinen P, Saarela J, Kallioniemi OP, Monni O. Are data from different gene expression microarray platforms comparable?. Genomics 2004, 83(6):1164-1168. 10.1016/j.ygeno.2004.01.004, 15177569.
    • (2004) Genomics , vol.83 , Issue.6 , pp. 1164-1168
    • Jarvinen, A.K.1    Hautaniemi, S.2    Edgren, H.3    Auvinen, P.4    Saarela, J.5    Kallioniemi, O.P.6    Monni, O.7
  • 27
    • 10244224128 scopus 로고    scopus 로고
    • Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies
    • 10.1093/bioinformatics/bth381, 15231529
    • Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics 2004, 20(17):3166-3178. 10.1093/bioinformatics/bth381, 15231529.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3166-3178
    • Wang, J.1    Coombes, K.R.2    Highsmith, W.E.3    Keating, M.J.4    Abruzzo, L.V.5
  • 28
    • 33646052085 scopus 로고    scopus 로고
    • Pooling information across different studies and oligonucleotide microarray chip types to identify prognostic genes for lung cancer
    • New York: Springer-Verlag
    • Morris JS, Yin G, Baggerly KA, Wu C, Zhang L. Pooling information across different studies and oligonucleotide microarray chip types to identify prognostic genes for lung cancer. Methods of Microarray Data Analysis IV 2005, 51-664. New York: Springer-Verlag.
    • (2005) Methods of Microarray Data Analysis IV , pp. 51-664
    • Morris, J.S.1    Yin, G.2    Baggerly, K.A.3    Wu, C.4    Zhang, L.5
  • 30
    • 13244289883 scopus 로고    scopus 로고
    • Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes
    • 10.1186/1471-2105-5-81, 476733, 15217521
    • Jiang H, Deng Y, Chen HS, Tao L, Sha Q, Chen J, Tsai CJ, Zhang S. Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics 2004, 5:81. 10.1186/1471-2105-5-81, 476733, 15217521.
    • (2004) BMC Bioinformatics , vol.5 , pp. 81
    • Jiang, H.1    Deng, Y.2    Chen, H.S.3    Tao, L.4    Sha, Q.5    Chen, J.6    Tsai, C.J.7    Zhang, S.8
  • 31
    • 34447528847 scopus 로고    scopus 로고
    • Novel and simple transformation algorithm for combining microarray data sets
    • 10.1186/1471-2105-8-218, 1914088, 17588268
    • Kim KY, Ki DH, Jeong HJ, Jeung HC, Chung HC, Rha SY. Novel and simple transformation algorithm for combining microarray data sets. BMC Bioinformatics 2007, 8:218. 10.1186/1471-2105-8-218, 1914088, 17588268.
    • (2007) BMC Bioinformatics , vol.8 , pp. 218
    • Kim, K.Y.1    Ki, D.H.2    Jeong, H.J.3    Jeung, H.C.4    Chung, H.C.5    Rha, S.Y.6
  • 32
    • 33747874717 scopus 로고    scopus 로고
    • Combining multiple microarrays in the presence of controlling variables
    • 10.1093/bioinformatics/btl183, 16705015
    • Park T, Yi SG, Shin YK, Lee S. Combining multiple microarrays in the presence of controlling variables. Bioinformatics 2006, 22(14):1682-1689. 10.1093/bioinformatics/btl183, 16705015.
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. 1682-1689
    • Park, T.1    Yi, S.G.2    Shin, Y.K.3    Lee, S.4
  • 33
    • 42649134796 scopus 로고    scopus 로고
    • Merging two gene-expression studies via cross-platform normalization
    • 10.1093/bioinformatics/btn083, 18325927
    • Shabalin AA, Tjelmeland H, Fan C, Perou CM, Nobel AB. Merging two gene-expression studies via cross-platform normalization. Bioinformatics 2008, 24(9):1154-1160. 10.1093/bioinformatics/btn083, 18325927.
    • (2008) Bioinformatics , vol.24 , Issue.9 , pp. 1154-1160
    • Shabalin, A.A.1    Tjelmeland, H.2    Fan, C.3    Perou, C.M.4    Nobel, A.B.5
  • 34
    • 25444515422 scopus 로고    scopus 로고
    • Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    • 10.1186/1471-2105-6-107, 1127107, 15850491
    • Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 2005, 6:107. 10.1186/1471-2105-6-107, 1127107, 15850491.
    • (2005) BMC Bioinformatics , vol.6 , pp. 107
    • Carter, S.L.1    Eklund, A.C.2    Mecham, B.H.3    Kohane, I.S.4    Szallasi, Z.5
  • 35
    • 34247349497 scopus 로고    scopus 로고
    • Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays
    • 10.1186/1471-2105-8-108, 1853115, 17394657
    • Lu J, Lee JC, Salit ML, Cam MC. Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. BMC Bioinformatics 2007, 8:108. 10.1186/1471-2105-8-108, 1853115, 17394657.
    • (2007) BMC Bioinformatics , vol.8 , pp. 108
    • Lu, J.1    Lee, J.C.2    Salit, M.L.3    Cam, M.C.4
  • 36
    • 2442691827 scopus 로고    scopus 로고
    • Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
    • 10.1093/nar/gnh071, 419626, 15161944
    • Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 2004, 32(9):e74. 10.1093/nar/gnh071, 419626, 15161944.
    • (2004) Nucleic Acids Res , vol.32 , Issue.9
    • Mecham, B.H.1    Klus, G.T.2    Strovel, J.3    Augustus, M.4    Byrne, D.5    Bozso, P.6    Wetmore, D.Z.7    Mariani, T.J.8    Kohane, I.S.9    Szallasi, Z.10
  • 37
    • 78149413202 scopus 로고    scopus 로고
    • Alternative probeset definitions for combining microarray data across studies using different versions of affymetrix oligonucleotide arrays
    • New York: Chapman-Hall
    • Morris JS, Wu C, Coombes KR, Baggerly KA, Wang J, Zhang L. Alternative probeset definitions for combining microarray data across studies using different versions of affymetrix oligonucleotide arrays. Meta-Analysis in Genetics 2006, 1-214. New York: Chapman-Hall.
    • (2006) Meta-Analysis in Genetics , pp. 1-214
    • Morris, J.S.1    Wu, C.2    Coombes, K.R.3    Baggerly, K.A.4    Wang, J.5    Zhang, L.6
  • 38
    • 0036211063 scopus 로고    scopus 로고
    • Analysis of matched mRNA measurements from two different microarray technologies
    • 10.1093/bioinformatics/18.3.405, 11934739
    • Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002, 18(3):405-412. 10.1093/bioinformatics/18.3.405, 11934739.
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 405-412
    • Kuo, W.P.1    Jenssen, T.K.2    Butte, A.J.3    Ohno-Machado, L.4    Kohane, I.S.5
  • 39
    • 53149135477 scopus 로고    scopus 로고
    • Key issues in conducting a meta-analysis of gene expression microarray datasets
    • 10.1371/journal.pmed.0050184, 2528050, 18767902
    • Ramasamy A, Mondry A, Holmes CC, Altman DG. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 2008, 5(9):e184. 10.1371/journal.pmed.0050184, 2528050, 18767902.
    • (2008) PLoS Med , vol.5 , Issue.9
    • Ramasamy, A.1    Mondry, A.2    Holmes, C.C.3    Altman, D.G.4
  • 40
    • 1542309545 scopus 로고    scopus 로고
    • Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer
    • 10.1007/s10142-003-0087-5, 12884057
    • Ghosh D, Barette TR, Rhodes D, Chinnaiyan AM. Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics 2003, 3(4):180-188. 10.1007/s10142-003-0087-5, 12884057.
    • (2003) Funct Integr Genomics , vol.3 , Issue.4 , pp. 180-188
    • Ghosh, D.1    Barette, T.R.2    Rhodes, D.3    Chinnaiyan, A.M.4
  • 41
    • 4944232237 scopus 로고    scopus 로고
    • Combining multiple microarray studies and modeling interstudy variation
    • 10.1093/bioinformatics/btg1010, 12855442
    • Choi JK, Yu U, Kim S, Yoo OJ. Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 2003, 19(Suppl 1):i84-90. 10.1093/bioinformatics/btg1010, 12855442.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Choi, J.K.1    Yu, U.2    Kim, S.3    Yoo, O.J.4
  • 42
    • 25444521278 scopus 로고    scopus 로고
    • Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
    • 10.1186/1471-2105-6-128, 1173085, 15921507
    • Hu P, Greenwood CM, Beyene J. Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. BMC Bioinformatics 2005, 6:128. 10.1186/1471-2105-6-128, 1173085, 15921507.
    • (2005) BMC Bioinformatics , vol.6 , pp. 128
    • Hu, P.1    Greenwood, C.M.2    Beyene, J.3
  • 43
    • 18844392338 scopus 로고    scopus 로고
    • Combining Affymetrix microarray results
    • 10.1186/1471-2105-6-57, 1274254, 15774008
    • Stevens JR, Doerge RW. Combining Affymetrix microarray results. BMC Bioinformatics 2005, 6:57. 10.1186/1471-2105-6-57, 1274254, 15774008.
    • (2005) BMC Bioinformatics , vol.6 , pp. 57
    • Stevens, J.R.1    Doerge, R.W.2
  • 44
    • 34147103409 scopus 로고    scopus 로고
    • Bayesian meta-analysis models for microarray data: a comparative study
    • 10.1186/1471-2105-8-80, 1851021, 17343745
    • Conlon EM, Song JJ, Liu A. Bayesian meta-analysis models for microarray data: a comparative study. BMC Bioinformatics 2007, 8:80. 10.1186/1471-2105-8-80, 1851021, 17343745.
    • (2007) BMC Bioinformatics , vol.8 , pp. 80
    • Conlon, E.M.1    Song, J.J.2    Liu, A.3
  • 45
    • 55449121996 scopus 로고    scopus 로고
    • Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration
    • 10.1186/1471-2105-9-354, 2579308, 18755028
    • Liang Y, Kelemen A. Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration. BMC Bioinformatics 2008, 9:354. 10.1186/1471-2105-9-354, 2579308, 18755028.
    • (2008) BMC Bioinformatics , vol.9 , pp. 354
    • Liang, Y.1    Kelemen, A.2
  • 46
    • 67651165147 scopus 로고    scopus 로고
    • Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach
    • 10.1089/omi.2008.0074, 19445647
    • Nguyen TT, Nowakowski RS, Androulakis IP. Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach. Omics 2009, 13(3):219-237. 10.1089/omi.2008.0074, 19445647.
    • (2009) Omics , vol.13 , Issue.3 , pp. 219-237
    • Nguyen, T.T.1    Nowakowski, R.S.2    Androulakis, I.P.3
  • 47
    • 0038724494 scopus 로고    scopus 로고
    • Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data
    • Monti STP, Mesirov J, Golub T. Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data. Mach Learn 2003, 52:91-118.
    • (2003) Mach Learn , vol.52 , pp. 91-118
    • Monti, S.T.P.1    Mesirov, J.2    Golub, T.3
  • 48
    • 36749055295 scopus 로고    scopus 로고
    • Determining the number of clusters using the weighted gap statistic
    • 10.1111/j.1541-0420.2007.00784.x, 17425640
    • Yan M, Ye K. Determining the number of clusters using the weighted gap statistic. Biometrics 2007, 63(4):1031-1037. 10.1111/j.1541-0420.2007.00784.x, 17425640.
    • (2007) Biometrics , vol.63 , Issue.4 , pp. 1031-1037
    • Yan, M.1    Ye, K.2
  • 49
    • 33846606051 scopus 로고    scopus 로고
    • Clustering methods for microarray gene expression data
    • 10.1089/omi.2006.10.507, 17233561
    • Belacel N, Wang Q, Cuperlovic-Culf M. Clustering methods for microarray gene expression data. OMICS 2006, 10(4):507-531. 10.1089/omi.2006.10.507, 17233561.
    • (2006) OMICS , vol.10 , Issue.4 , pp. 507-531
    • Belacel, N.1    Wang, Q.2    Cuperlovic-Culf, M.3
  • 50
    • 25444485685 scopus 로고    scopus 로고
    • Adding confidence to gene expression clustering
    • 10.1534/genetics.104.031500, 1449753, 15944369
    • Munneke B, Schlauch KA, Simonsen KL, Beavis WD, Doerge RW. Adding confidence to gene expression clustering. Genetics 2005, 170(4):2003-2011. 10.1534/genetics.104.031500, 1449753, 15944369.
    • (2005) Genetics , vol.170 , Issue.4 , pp. 2003-2011
    • Munneke, B.1    Schlauch, K.A.2    Simonsen, K.L.3    Beavis, W.D.4    Doerge, R.W.5
  • 51
    • 0041965980 scopus 로고    scopus 로고
    • Cluster Ensembles A Knowledge Reuse Framework for Combining Multiple Partitions
    • Strehl A, Ghosh J. Cluster Ensembles A Knowledge Reuse Framework for Combining Multiple Partitions. Journal on Machine Learning Research 2002, 3:583-617.
    • (2002) Journal on Machine Learning Research , vol.3 , pp. 583-617
    • Strehl, A.1    Ghosh, J.2
  • 52
    • 3042686005 scopus 로고    scopus 로고
    • Bayesian mixture model based clustering of replicated microarray data
    • 10.1093/bioinformatics/bth068, 14871871
    • Medvedovic M, Yeung KY, Bumgarner RE. Bayesian mixture model based clustering of replicated microarray data. Bioinformatics 2004, 20(8):1222-1232. 10.1093/bioinformatics/bth068, 14871871.
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1222-1232
    • Medvedovic, M.1    Yeung, K.Y.2    Bumgarner, R.E.3
  • 53
    • 0037667290 scopus 로고    scopus 로고
    • Clustering gene-expression data with repeated measurements
    • 10.1186/gb-2003-4-5-r34, 156590, 12734014
    • Yeung KY, Medvedovic M, Bumgarner RE. Clustering gene-expression data with repeated measurements. Genome Biol 2003, 4(5):R34. 10.1186/gb-2003-4-5-r34, 156590, 12734014.
    • (2003) Genome Biol , vol.4 , Issue.5
    • Yeung, K.Y.1    Medvedovic, M.2    Bumgarner, R.E.3
  • 55
    • 0036798238 scopus 로고    scopus 로고
    • Judging the quality of gene expression-based clustering methods using gene annotation
    • 10.1101/gr.397002, 187526, 12368250
    • Gibbons FD, Roth FP. Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res 2002, 12(10):1574-1581. 10.1101/gr.397002, 187526, 12368250.
    • (2002) Genome Res , vol.12 , Issue.10 , pp. 1574-1581
    • Gibbons, F.D.1    Roth, F.P.2
  • 57
    • 84888285521 scopus 로고    scopus 로고
    • Mclust: Model-Based Clustering/Normal Mixture Modeling
    • Fraley A. mclust: Model-Based Clustering/Normal Mixture Modeling. R packages 2007,
    • (2007) R packages
    • Fraley, A.1
  • 59
    • 0030305457 scopus 로고    scopus 로고
    • R: A Language for Data Analysis and Graphics
    • Ihaka R, Gentleman R. R: A Language for Data Analysis and Graphics. J Comp Graphical Statistics 1996, 5(3):299-314., http://www.R-project.org
    • (1996) J Comp Graphical Statistics , vol.5 , Issue.3 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 61
    • 84888285244 scopus 로고    scopus 로고
    • Som: Self-Organizing Map
    • Yan J. som: Self-Organizing Map. R packages 2004,
    • (2004) R packages
    • Yan, J.1
  • 62
    • 34247250323 scopus 로고    scopus 로고
    • Consensus framework for exploring microarray data using multiple clustering methods
    • 10.1089/omi.2006.0008, 17411399
    • Laderas T, McWeeney S. Consensus framework for exploring microarray data using multiple clustering methods. Omics 2007, 11(1):116-128. 10.1089/omi.2006.0008, 17411399.
    • (2007) Omics , vol.11 , Issue.1 , pp. 116-128
    • Laderas, T.1    McWeeney, S.2
  • 63
    • 24944539029 scopus 로고    scopus 로고
    • Consensus clustering and functional interpretation of gene-expression data
    • 10.1186/gb-2004-5-11-r94, 545785, 15535870
    • Swift S, Tucker A, Vinciotti V, Martin N, Orengo C, Liu X, Kellam P. Consensus clustering and functional interpretation of gene-expression data. Genome Biol 2004, 5(11):R94. 10.1186/gb-2004-5-11-r94, 545785, 15535870.
    • (2004) Genome Biol , vol.5 , Issue.11
    • Swift, S.1    Tucker, A.2    Vinciotti, V.3    Martin, N.4    Orengo, C.5    Liu, X.6    Kellam, P.7
  • 64
    • 84888285697 scopus 로고    scopus 로고
    • Genomatix
    • Genomatix. , http://www.genomatix.de
  • 65
    • 19844377004 scopus 로고    scopus 로고
    • Identification of functional transcription factor binding sites using closely related Saccharomyces species
    • 10.1101/gr.3578205, 1088298, 15837806
    • Doniger SW, Huh J, Fay JC. Identification of functional transcription factor binding sites using closely related Saccharomyces species. Genome Res 2005, 15(5):701-709. 10.1101/gr.3578205, 1088298, 15837806.
    • (2005) Genome Res , vol.15 , Issue.5 , pp. 701-709
    • Doniger, S.W.1    Huh, J.2    Fay, J.C.3
  • 66
    • 0034284481 scopus 로고    scopus 로고
    • Conserved noncoding sequences are reliable guides to regulatory elements
    • 10.1016/S0168-9525(00)02081-3, 10973062
    • Hardison RC. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 2000, 16(9):369-372. 10.1016/S0168-9525(00)02081-3, 10973062.
    • (2000) Trends Genet , vol.16 , Issue.9 , pp. 369-372
    • Hardison, R.C.1
  • 67
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
    • 10.1093/bioinformatics/15.3.211, 10222408
    • Morgenstern B. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15(3):211-218. 10.1093/bioinformatics/15.3.211, 10222408.
    • (1999) Bioinformatics , vol.15 , Issue.3 , pp. 211-218
    • Morgenstern, B.1
  • 68
    • 13244259261 scopus 로고    scopus 로고
    • DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors
    • 10.1186/1471-2105-5-128, 520757, 15357879
    • Schmollinger M, Nieselt K, Kaufmann M, Morgenstern B. DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics 2004, 5:128. 10.1186/1471-2105-5-128, 520757, 15357879.
    • (2004) BMC Bioinformatics , vol.5 , pp. 128
    • Schmollinger, M.1    Nieselt, K.2    Kaufmann, M.3    Morgenstern, B.4
  • 69
    • 2942516151 scopus 로고    scopus 로고
    • Benchmarking tools for the alignment of functional noncoding DNA
    • 10.1186/1471-2105-5-6, 344529, 14736341
    • Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5:6. 10.1186/1471-2105-5-6, 344529, 14736341.
    • (2004) BMC Bioinformatics , vol.5 , pp. 6
    • Pollard, D.A.1    Bergman, C.M.2    Stoye, J.3    Celniker, S.E.4    Eisen, M.B.5
  • 71
    • 50849114182 scopus 로고    scopus 로고
    • Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array
    • 10.1186/1471-2164-9-349, 2527337, 18655706
    • Singer GA, Wu J, Yan P, Plass C, Huang TH, Davuluri RV. Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. BMC Genomics 2008, 9:349. 10.1186/1471-2164-9-349, 2527337, 18655706.
    • (2008) BMC Genomics , vol.9 , pp. 349
    • Singer, G.A.1    Wu, J.2    Yan, P.3    Plass, C.4    Huang, T.H.5    Davuluri, R.V.6
  • 72
    • 0000008146 scopus 로고
    • Comparing partitions
    • Hubert L, Arabie P. Comparing partitions. J Classification 1985, 2(1):193-218.
    • (1985) J Classification , vol.2 , Issue.1 , pp. 193-218
    • Hubert, L.1    Arabie, P.2
  • 73
    • 77952610908 scopus 로고    scopus 로고
    • Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver
    • (accepted)
    • Nguyen TT, Almon RR, DuBois DC, Jusko WJ, Androulakis IP. Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver. BMC Bioinformatics 2010, (accepted).
    • (2010) BMC Bioinformatics
    • Nguyen, T.T.1    Almon, R.R.2    DuBois, D.C.3    Jusko, W.J.4    Androulakis, I.P.5
  • 74
    • 0242302280 scopus 로고    scopus 로고
    • Using ANOVA for gene selection from microarray studies of the nervous system
    • 10.1016/S1046-2023(03)00157-9, 14597312
    • Pavlidis P. Using ANOVA for gene selection from microarray studies of the nervous system. Methods 2003, 31(4):282-289. 10.1016/S1046-2023(03)00157-9, 14597312.
    • (2003) Methods , vol.31 , Issue.4 , pp. 282-289
    • Pavlidis, P.1
  • 75
    • 29144470990 scopus 로고    scopus 로고
    • Topology, tinkering and evolution of the human transcription factor network
    • 10.1111/j.1742-4658.2005.05041.x, 16336278
    • Rodriguez-Caso C, Medina MA, Sole RV. Topology, tinkering and evolution of the human transcription factor network. Febs J 2005, 272(24):6423-6434. 10.1111/j.1742-4658.2005.05041.x, 16336278.
    • (2005) Febs J , vol.272 , Issue.24 , pp. 6423-6434
    • Rodriguez-Caso, C.1    Medina, M.A.2    Sole, R.V.3
  • 76
    • 33747497812 scopus 로고    scopus 로고
    • ETS transcription factors and regulation of immunity
    • 10.1007/s00005-006-0017-z, 16652219
    • Gallant S, Gilkeson G. ETS transcription factors and regulation of immunity. Arch Immunol Ther Exp (Warsz) 2006, 54(3):149-163. 10.1007/s00005-006-0017-z, 16652219.
    • (2006) Arch Immunol Ther Exp (Warsz) , vol.54 , Issue.3 , pp. 149-163
    • Gallant, S.1    Gilkeson, G.2
  • 77
    • 8544265317 scopus 로고    scopus 로고
    • Forkhead-box transcription factors and their role in the immune system
    • 10.1038/nri1488, 15516968
    • Coffer PJ, Burgering BM. Forkhead-box transcription factors and their role in the immune system. Nat Rev Immunol 2004, 4(11):889-899. 10.1038/nri1488, 15516968.
    • (2004) Nat Rev Immunol , vol.4 , Issue.11 , pp. 889-899
    • Coffer, P.J.1    Burgering, B.M.2
  • 78
    • 0034464826 scopus 로고    scopus 로고
    • CBP (CREB binding protein) integrates NF-kappaB (nuclear factor-kappaB) and glucocorticoid receptor physical interactions and antagonism
    • 10.1210/me.14.8.1222, 10935546
    • McKay LI, Cidlowski JA. CBP (CREB binding protein) integrates NF-kappaB (nuclear factor-kappaB) and glucocorticoid receptor physical interactions and antagonism. Mol Endocrinol 2000, 14(8):1222-1234. 10.1210/me.14.8.1222, 10935546.
    • (2000) Mol Endocrinol , vol.14 , Issue.8 , pp. 1222-1234
    • McKay, L.I.1    Cidlowski, J.A.2
  • 79
    • 0036432834 scopus 로고    scopus 로고
    • The role of CREB and other transcription factors in the pharmacotherapy and etiology of depression
    • 10.1080/078538902320772106, 12452479
    • Sulser F. The role of CREB and other transcription factors in the pharmacotherapy and etiology of depression. Ann Med 2002, 34(5):348-356. 10.1080/078538902320772106, 12452479.
    • (2002) Ann Med , vol.34 , Issue.5 , pp. 348-356
    • Sulser, F.1
  • 80
    • 9444285520 scopus 로고    scopus 로고
    • Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system
    • 10.1186/1471-2164-5-82, 534115, 15504237
    • Hutton JJ, Jegga AG, Kong S, Gupta A, Ebert C, Williams S, Katz JD, Aronow BJ. Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system. BMC Genomics 2004, 5(1):82. 10.1186/1471-2164-5-82, 534115, 15504237.
    • (2004) BMC Genomics , vol.5 , Issue.1 , pp. 82
    • Hutton, J.J.1    Jegga, A.G.2    Kong, S.3    Gupta, A.4    Ebert, C.5    Williams, S.6    Katz, J.D.7    Aronow, B.J.8
  • 81
    • 23444431623 scopus 로고    scopus 로고
    • Retinoid x receptor heterodimers in the metabolic syndrome
    • 10.1056/NEJMra043590, 16093469
    • Shulman AI, Mangelsdorf DJ. Retinoid x receptor heterodimers in the metabolic syndrome. N Engl J Med 2005, 353(6):604-615. 10.1056/NEJMra043590, 16093469.
    • (2005) N Engl J Med , vol.353 , Issue.6 , pp. 604-615
    • Shulman, A.I.1    Mangelsdorf, D.J.2
  • 82
    • 37349100520 scopus 로고    scopus 로고
    • The FoxO transcription factors and metabolic regulation
    • 10.1016/j.febslet.2007.11.025, 18022395
    • Nakae J, Oki M, Cao Y. The FoxO transcription factors and metabolic regulation. FEBS Lett 2008, 582(1):54-67. 10.1016/j.febslet.2007.11.025, 18022395.
    • (2008) FEBS Lett , vol.582 , Issue.1 , pp. 54-67
    • Nakae, J.1    Oki, M.2    Cao, Y.3
  • 83
    • 49549105302 scopus 로고    scopus 로고
    • A critical role of Sp1 transcription factor in regulating gene expression in response to insulin and other hormones
    • 10.1016/j.lfs.2008.06.024, 18664368
    • Solomon SS, Majumdar G, Martinez-Hernandez A, Raghow R. A critical role of Sp1 transcription factor in regulating gene expression in response to insulin and other hormones. Life Sci 2008, 83(9-10):305-312. 10.1016/j.lfs.2008.06.024, 18664368.
    • (2008) Life Sci , vol.83 , Issue.9-10 , pp. 305-312
    • Solomon, S.S.1    Majumdar, G.2    Martinez-Hernandez, A.3    Raghow, R.4
  • 84
    • 0034035667 scopus 로고    scopus 로고
    • Hepatocyte-specific mutation establishes retinoid X receptor alpha as a heterodimeric integrator of multiple physiological processes in the liver
    • 10.1128/MCB.20.12.4436-4444.2000, 85811, 10825207
    • Wan YJ, An D, Cai Y, Repa JJ, Hung-Po T, Flores M, Postic C, Magnuson MA, Chen J, Chien KR, et al. Hepatocyte-specific mutation establishes retinoid X receptor alpha as a heterodimeric integrator of multiple physiological processes in the liver. Mol Cell Biol 2000, 20(12):4436-4444. 10.1128/MCB.20.12.4436-4444.2000, 85811, 10825207.
    • (2000) Mol Cell Biol , vol.20 , Issue.12 , pp. 4436-4444
    • Wan, Y.J.1    An, D.2    Cai, Y.3    Repa, J.J.4    Hung-Po, T.5    Flores, M.6    Postic, C.7    Magnuson, M.A.8    Chen, J.9    Chien, K.R.10
  • 85
    • 0346243568 scopus 로고    scopus 로고
    • ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research
    • 1241745, 14630514
    • Tong W, Cao X, Harris S, Sun H, Fang H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, et al. ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect 2003, 111(15):1819-1826. 1241745, 14630514.
    • (2003) Environ Health Perspect , vol.111 , Issue.15 , pp. 1819-1826
    • Tong, W.1    Cao, X.2    Harris, S.3    Sun, H.4    Fang, H.5    Fuscoe, J.6    Harris, A.7    Hong, H.8    Xie, Q.9    Perkins, R.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.