메뉴 건너뛰기




Volumn 10, Issue 3, 2013, Pages 303-315

Zebrafish expression ontology of gene sets (ZEOGS): A tool to analyze enrichment of zebrafish anatomical terms in large gene sets

Author keywords

[No Author keywords available]

Indexed keywords

BECLOMETASONE; GLUCOCORTICOID; GLUCOCORTICOID RECEPTOR;

EID: 84883353665     PISSN: 15458547     EISSN: None     Source Type: Journal    
DOI: 10.1089/zeb.2012.0865     Document Type: Article
Times cited : (10)

References (50)
  • 1
    • 27744515738 scopus 로고    scopus 로고
    • New ways to admire zebrafish: Progress in functional genomics research methodology
    • Teh C, Parinov S, Korzh V. New ways to admire zebrafish: progress in functional genomics research methodology. Biotechniques 2005;38:897-906.
    • (2005) Biotechniques , vol.38 , pp. 897-906
    • Teh, C.1    Parinov, S.2    Korzh, V.3
  • 5
    • 38549118463 scopus 로고    scopus 로고
    • The Zebrafish Information Network: The zebrafish model organism database provides expanded support for genotypes and phenotypes
    • Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, et al. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 2008;36:D768-D772.
    • (2008) Nucleic Acids Res , vol.36
    • Sprague, J.1    Bayraktaroglu, L.2    Bradford, Y.3    Conlin, T.4    Dunn, N.5    Fashena, D.6
  • 7
    • 73649135187 scopus 로고    scopus 로고
    • Developmental anatomy ontology of zebrafish: An integrative semantic framework
    • Belmamoune M, Verbeek FJ. Developmental anatomy ontology of zebrafish: an integrative semantic framework. J Integr Bioinform 2007;4:65.
    • (2007) J Integr Bioinform , vol.4 , pp. 65
    • Belmamoune, M.1    Verbeek, F.J.2
  • 11
    • 77955921846 scopus 로고    scopus 로고
    • The zebrafish as an in vivo model system for glucocorticoid resistance
    • Schoonheim PJ, Chatzopoulou A, Schaaf MJ. The zebrafish as an in vivo model system for glucocorticoid resistance. Steroids 2010;75:918-925.
    • (2010) Steroids , vol.75 , pp. 918-925
    • Schoonheim, P.J.1    Chatzopoulou, A.2    Schaaf, M.J.3
  • 13
    • 53849143575 scopus 로고    scopus 로고
    • Tissue-specific glucocorticoid action: A family affair
    • Gross KL, Cidlowski JA. Tissue-specific glucocorticoid action: a family affair. Trends Endocrinol Metab 2008;19:331-339.
    • (2008) Trends Endocrinol Metab , vol.19 , pp. 331-339
    • Gross, K.L.1    Cidlowski, J.A.2
  • 14
    • 0004113253 scopus 로고    scopus 로고
    • A Guide for the Laboratory Use of the Zebrafish (Danio rerio), 4th edn. Eugene, OR: University of Oregon Press
    • Westerfield M. The Zebrafish Book. A Guide for the Laboratory Use of the Zebrafish (Danio rerio), 4th edn. Eugene, OR: University of Oregon Press, 2000.
    • (2000) The Zebrafish Book
    • Westerfield, M.1
  • 17
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Article3
    • Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004;3:Article3.
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 18
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth GK, Speed T. Normalization of cDNA microarray data. Methods 2003;31:265-273.
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 19
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Methodol) 1995;57:289-300.
    • (1995) J R Stat Soc ser B (Methodol) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 20
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and bioconductor: A powerful link between biological databases and microarray data analysis
    • Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W. BioMart and bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005;21:3439-3440.
    • (2005) Bioinformatics , vol.21 , pp. 3439-3440
    • Durinck, S.1    Moreau, Y.2    Kasprzyk, A.3    Davis, S.4    De Moor, B.5    Brazma, A.6    Huber, W.7
  • 21
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W, Sherman BT, Lempicki RA. 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
  • 22
    • 33847751090 scopus 로고    scopus 로고
    • Gene expression profiling of zebrafish embryonic retinal pigment epithelium in vivo
    • Leung YF, Ma P, Dowling JE. Gene expression profiling of zebrafish embryonic retinal pigment epithelium in vivo. Invest Ophthalmol Vis Sci 2007;48:881-890.
    • (2007) Invest Ophthalmol Vis Sci , vol.48 , pp. 881-890
    • Leung, Y.F.1    Ma, P.2    Dowling, J.E.3
  • 23
    • 33750465839 scopus 로고    scopus 로고
    • Genomewide expression profiling in the zebrafish embryo identifies target genes regulated by Hedgehog signaling during vertebrate development
    • Xu J, Srinivas BP, Tay SY, Mak A, Yu X, Lee SG, et al. Genomewide expression profiling in the zebrafish embryo identifies target genes regulated by Hedgehog signaling during vertebrate development. Genetics 2006;174:735-752.
    • (2006) Genetics , vol.174 , pp. 735-752
    • Xu, J.1    Srinivas, B.P.2    Tay, S.Y.3    Mak, A.4    Yu, X.5    Lee, S.G.6
  • 25
    • 77956481552 scopus 로고    scopus 로고
    • Role of glucocorticoids and the glucocorticoid receptor in metabolism: Insights from genetic manipulations
    • Rose AJ, Vegiopoulos A, Herzig S. Role of glucocorticoids and the glucocorticoid receptor in metabolism: insights from genetic manipulations. J Steroid Biochem Mol Biol 2010;122:10-20.
    • (2010) J Steroid Biochem Mol Biol , vol.122 , pp. 10-20
    • Rose, A.J.1    Vegiopoulos, A.2    Herzig, S.3
  • 26
    • 80555156759 scopus 로고    scopus 로고
    • Glucocorticoid receptor- mediated apoptosis: Mechanisms of resistance in cancer cells
    • Schlossmacher G, Stevens A, White A. Glucocorticoid receptor- mediated apoptosis: mechanisms of resistance in cancer cells. J Endocrinol 2011;211:17-25.
    • (2011) J Endocrinol , vol.211 , pp. 17-25
    • Schlossmacher, G.1    Stevens, A.2    White, A.3
  • 29
    • 80052047742 scopus 로고    scopus 로고
    • Dexamethasone induces transcriptional activation of Bcl-xL gene and inhibits cardiac injury by myocardial ischemia
    • Xu B, Strom J, Chen QM. Dexamethasone induces transcriptional activation of Bcl-xL gene and inhibits cardiac injury by myocardial ischemia. Eur J Pharmacol 2011;668:194-200.
    • (2011) Eur J Pharmacol , vol.668 , pp. 194-200
    • Xu, B.1    Strom, J.2    Chen, Q.M.3
  • 30
    • 79958773563 scopus 로고    scopus 로고
    • Knockout of the vascular endothelial glucocorticoid receptor abrogates dexamethasone-induced hypertension
    • Goodwin JE, Zhang J, Gonzalez D, Albinsson S, Geller DS. Knockout of the vascular endothelial glucocorticoid receptor abrogates dexamethasone-induced hypertension. J Hypertens 2011;29:1347-1356.
    • (2011) J Hypertens , vol.29 , pp. 1347-1356
    • Goodwin, J.E.1    Zhang, J.2    Gonzalez, D.3    Albinsson, S.4    Geller, D.S.5
  • 32
    • 66849128246 scopus 로고    scopus 로고
    • Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism
    • Yoshikawa N, Nagasaki M, Sano M, Tokudome S, Ueno K, Shimizu N, et al. Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. Am J Physiol Endocrinol Metab 2009;296:E1363-E1373.
    • (2009) Am J Physiol Endocrinol Metab , vol.296
    • Yoshikawa, N.1    Nagasaki, M.2    Sano, M.3    Tokudome, S.4    Ueno, K.5    Shimizu, N.6
  • 35
    • 0028701616 scopus 로고
    • Glial and neuronal glucocorticoid receptor immunoreactive cell populations in developing, adult, and aging brain
    • discussion 61-43
    • Cintra A, Bhatnagar M, Chadi G, Tinner B, Lindberg J, Gustafsson JA, et al. Glial and neuronal glucocorticoid receptor immunoreactive cell populations in developing, adult, and aging brain. Ann N Y Acad Sci 1994;746:42-61; discussion 61-43.
    • (1994) Ann N y Acad Sci , vol.746 , pp. 42-61
    • Cintra, A.1    Bhatnagar, M.2    Chadi, G.3    Tinner, B.4    Lindberg, J.5    Gustafsson, J.A.6
  • 37
    • 0029934419 scopus 로고    scopus 로고
    • Apparent mineralocorticoid excess: Genotype is correlated with biochemical phenotype
    • Mune T, White PC. Apparent mineralocorticoid excess: genotype is correlated with biochemical phenotype. Hypertension 1996;27:1193-1199.
    • (1996) Hypertension , vol.27 , pp. 1193-1199
    • Mune, T.1    White, P.C.2
  • 38
    • 0016590014 scopus 로고
    • Studies on the hepatic glucocorticoid receptor and on the hormonal modulation of specific mRNA levels during enzyme induction
    • Feigelson P, Beato M, Colman P, Kalimi M, Killewich LA, Schutz G. Studies on the hepatic glucocorticoid receptor and on the hormonal modulation of specific mRNA levels during enzyme induction. Recent Prog Horm Res 1975;31:213-242.
    • (1975) Recent Prog Horm Res , vol.31 , pp. 213-242
    • Feigelson, P.1    Beato, M.2    Colman, P.3    Kalimi, M.4    Killewich, L.A.5    Schutz, G.6
  • 39
    • 34547119052 scopus 로고    scopus 로고
    • Expression profiling of dexamethasone-treated primary chondrocytes identifies targets of glucocorticoid signalling in endochondral bone development
    • James CG, Ulici V, Tuckermann J, Underhill TM, Beier F. Expression profiling of dexamethasone-treated primary chondrocytes identifies targets of glucocorticoid signalling in endochondral bone development. BMC Genomics 2007;8:205.
    • (2007) BMC Genomics , vol.8 , pp. 205
    • James, C.G.1    Ulici, V.2    Tuckermann, J.3    Underhill, T.M.4    Beier, F.5
  • 40
    • 0031759740 scopus 로고    scopus 로고
    • Dexamethasone impairs growth hormone (GH)- stimulated growth by suppression of local insulin-like growth factor (IGF)-I production and expression of GH- and IGF-I-receptor in cultured rat chondrocytes
    • Jux C, Leiber K, Hugel U, Blum W, Ohlsson C, Klaus G, Mehls O. Dexamethasone impairs growth hormone (GH)- stimulated growth by suppression of local insulin-like growth factor (IGF)-I production and expression of GH- and IGF-I-receptor in cultured rat chondrocytes. Endocrinology 1998;139:3296-3305.
    • (1998) Endocrinology , vol.139 , pp. 3296-3305
    • Jux, C.1    Leiber, K.2    Hugel, U.3    Blum, W.4    Ohlsson, C.5    Klaus, G.6    Mehls, O.7
  • 41
    • 0346057833 scopus 로고    scopus 로고
    • Systemic and local regulation of the growth plate
    • van der Eerden BC, Karperien M, Wit JM. Systemic and local regulation of the growth plate. Endocr Rev 2003;24:782-801.
    • (2003) Endocr Rev , vol.24 , pp. 782-801
    • Van Der Eerden, B.C.1    Karperien, M.2    Wit, J.M.3
  • 42
    • 73649111416 scopus 로고    scopus 로고
    • Mechanisms of impaired growth: Effect of steroids on bone and cartilage
    • Olney RC. Mechanisms of impaired growth: effect of steroids on bone and cartilage. Horm Res 2009;72 Suppl 1:30-35.
    • (2009) Horm Res , vol.72 , Issue.SUPPL. 1 , pp. 30-35
    • Olney, R.C.1
  • 44
    • 15444363111 scopus 로고    scopus 로고
    • Corticosterone modulates noradrenaline-induced melatonin synthesis through inhibition of nuclear factor kappa B
    • Ferreira ZS, Fernandes PA, Duma D, Assreuy J, Avellar MC, Markus RP. Corticosterone modulates noradrenaline-induced melatonin synthesis through inhibition of nuclear factor kappa B. J Pineal Res 2005;38:182-188.
    • (2005) J Pineal Res , vol.38 , pp. 182-188
    • Ferreira, Z.S.1    Fernandes, P.A.2    Duma, D.3    Assreuy, J.4    Avellar, M.C.5    Markus, R.P.6
  • 45
    • 60349091250 scopus 로고    scopus 로고
    • The immunepineal axis: Stress as a modulator of pineal gland function
    • Couto-Moraes R, Palermo-Neto J, Markus RP. The immunepineal axis: stress as a modulator of pineal gland function. Ann N Y Acad Sci 2009;1153:193-202.
    • (2009) Ann N y Acad Sci , vol.1153 , pp. 193-202
    • Couto-Moraes, R.1    Palermo-Neto, J.2    Markus, R.P.3
  • 46
    • 33646468930 scopus 로고    scopus 로고
    • Chronic stress induces upregulation of brain-derived neurotrophic factor (BDNF) mRNA and integrin alpha5 expression in the rat pineal gland
    • Dagnino-Subiabre A, Zepeda-Carreno R, Diaz-Veliz G, Mora S, Aboitiz F. Chronic stress induces upregulation of brain-derived neurotrophic factor (BDNF) mRNA and integrin alpha5 expression in the rat pineal gland. Brain Res 2006;1086:27-34.
    • (2006) Brain Res , vol.1086 , pp. 27-34
    • Dagnino-Subiabre, A.1    Zepeda-Carreno, R.2    Diaz-Veliz, G.3    Mora, S.4    Aboitiz, F.5
  • 47
    • 68849113970 scopus 로고    scopus 로고
    • Microarray profiling reveals CXCR4a is downregulated by blood flow in vivo and mediates collateral formation in zebrafish embryos
    • Packham IM, Gray C, Heath PR, Hellewell PG, Ingham PW, Crossman DC, et al. Microarray profiling reveals CXCR4a is downregulated by blood flow in vivo and mediates collateral formation in zebrafish embryos. Physiol Genomics 2009;38:319-327.
    • (2009) Physiol Genomics , vol.38 , pp. 319-327
    • Packham, I.M.1    Gray, C.2    Heath, P.R.3    Hellewell, P.G.4    Ingham, P.W.5    Crossman, D.C.6
  • 48
    • 33847264343 scopus 로고    scopus 로고
    • Enrichment or depletion of a GO category within a class of genes: Which test?
    • Rivals I, Personnaz L, Taing L, Potier MC. Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics 2007;23:401-407.
    • (2007) Bioinformatics , vol.23 , pp. 401-407
    • Rivals, I.1    Personnaz, L.2    Taing, L.3    Potier, M.C.4
  • 49
    • 80053201210 scopus 로고    scopus 로고
    • The what, where, how and why of gene ontology - A primer for bioinformaticians
    • du Plessis L, Skunca N, Dessimoz C. The what, where, how and why of gene ontology - a primer for bioinformaticians. Brief Bioinform 2011;12:723-735.
    • (2011) Brief Bioinform , vol.12 , pp. 723-735
    • Du Plessis, L.1    Skunca, N.2    Dessimoz, C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.