메뉴 건너뛰기




Volumn 18, Issue 4, 2008, Pages 387-399

Differential expression analysis and regulatory network reconstruction for genes associated with muscle growth and adipose deposition in obese and lean pigs

Author keywords

Adipose deposition; Differential gene expression; Gene regulatory network (GRN); Muscle growth; Pathway focused microarray; Pig

Indexed keywords

ANALYSIS OF VARIANCE (ANOVA); BARIUM COMPOUNDS; BAYESIAN NETWORKS; CELL PROLIFERATION; FATTY ACIDS; GENE EXPRESSION; INFERENCE ENGINES; MAMMALS; MUSCLE; QUALITY CONTROL;

EID: 42549123230     PISSN: 10020071     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pnsc.2007.10.011     Document Type: Article
Times cited : (14)

References (49)
  • 1
    • 33748432086 scopus 로고    scopus 로고
    • Genetic correlations among fatty acid compositions in different sites of fat tissues, meat production, and meat quality traits in Duroc pigs
    • K. Suzuki M. Ishida H. Kadowaki Genetic correlations among fatty acid compositions in different sites of fat tissues, meat production, and meat quality traits in Duroc pigs J Anim Sci 84 8 2006 2026 2034
    • (2006) J Anim Sci , vol.84 , Issue.8 , pp. 2026-2034
    • Suzuki, K.1    Ishida, M.2    Kadowaki, H.3
  • 2
    • 33644509230 scopus 로고    scopus 로고
    • Quality pork genes and meat production
    • G.S. Plastow D. Carrión M. Gil Quality pork genes and meat production Meat Sci 70 3 2005 409 421
    • (2005) Meat Sci , vol.70 , Issue.3 , pp. 409-421
    • Plastow, G.S.1    Carrión, D.2    Gil, M.3
  • 3
    • 85120115266 scopus 로고    scopus 로고
    • Editorial Committee of “Pig Breeds in China”. Pig breeds in China. Shanghai: Scientific & Technical Publishers Press; 1986. p. 155–60 [in Chinese].
  • 4
    • 3242887152 scopus 로고    scopus 로고
    • Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
    • P. Khatri P. Bhavsar G. Bawa Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments Nucleic Acids Res 32 Web Server issue 2004 W449 W456
    • (2004) Nucleic Acids Res , vol.32 , Issue.Web Server issue , pp. W449-W456
    • Khatri, P.1    Bhavsar, P.2    Bawa, G.3
  • 5
    • 23144448699 scopus 로고    scopus 로고
    • GoPubMed: exploring PubMed with the Gene Ontology
    • A. Doms M. Schroeder GoPubMed: exploring PubMed with the Gene Ontology Nucleic Acids Res 33 Web Server issue 2005 W783 W786
    • (2005) Nucleic Acids Res , vol.33 , Issue.Web Server issue , pp. W783-W786
    • Doms, A.1    Schroeder, M.2
  • 6
    • 0036319960 scopus 로고    scopus 로고
    • Design issues for cDNA microarray experiments
    • Y.H. Yang T. Speed Design issues for cDNA microarray experiments Nat Rev Genet 3 8 2002 579 588
    • (2002) Nat Rev Genet , vol.3 , Issue.8 , pp. 579-588
    • Yang, Y.H.1    Speed, T.2
  • 7
    • 0036900895 scopus 로고    scopus 로고
    • Fundamentals of experimental design for cDNA microarrays
    • G.A. Churchill Fundamentals of experimental design for cDNA microarrays Nat Genet 32 Suppl. 2002 490 495
    • (2002) Nat Genet , vol.32 , Issue.Suppl. , pp. 490-495
    • Churchill, G.A.1
  • 8
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
    • Y.H. Yang S. Dudoit P. Luu Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 30 4 2002 15 24
    • (2002) Nucleic Acids Res , vol.30 , Issue.4 , pp. 15-24
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3
  • 9
    • 30044444274 scopus 로고    scopus 로고
    • WebArray: an online platform for microarray data analysis
    • X. Xia M. McClelland Y. Wang WebArray: an online platform for microarray data analysis BMC Bioinform 6 2005 306 311
    • (2005) BMC Bioinform , vol.6 , pp. 306-311
    • Xia, X.1    McClelland, M.2    Wang, Y.3
  • 10
    • 18744369640 scopus 로고    scopus 로고
    • Use of within-array replicate spots for assessing differential expression in microarray experiments
    • G.K. Smyth J. Michaud H.S. Scott Use of within-array replicate spots for assessing differential expression in microarray experiments Bioinformatics 21 9 2005 2067 2075
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2067-2075
    • Smyth, G.K.1    Michaud, J.2    Scott, H.S.3
  • 11
    • 0034960264 scopus 로고    scopus 로고
    • Missing value estimation methods for DNA microarrays
    • O. Troyanskaya M. Cantor G. Sherlock Missing value estimation methods for DNA microarrays Bioinformatics 17 6 2001 520 525
    • (2001) Bioinformatics , vol.17 , Issue.6 , pp. 520-525
    • Troyanskaya, O.1    Cantor, M.2    Sherlock, G.3
  • 12
    • 0035687554 scopus 로고    scopus 로고
    • Assessing gene significance from cDNA microarray expression data via mixed models
    • R.D. Wolfinger G. Gibson E.D. Wolfinger Assessing gene significance from cDNA microarray expression data via mixed models J Comput Biol 8 6 2001 625 637
    • (2001) J Comput Biol , vol.8 , Issue.6 , pp. 625-637
    • Wolfinger, R.D.1    Gibson, G.2    Wolfinger, E.D.3
  • 13
    • 24144445705 scopus 로고    scopus 로고
    • Improved statistical tests for differential gene expression by shrinking variance components estimates
    • X. Cui J.T. Hwang J. Qiu Improved statistical tests for differential gene expression by shrinking variance components estimates Biostatistics 6 1 2005 59 75
    • (2005) Biostatistics , vol.6 , Issue.1 , pp. 59-75
    • Cui, X.1    Hwang, J.T.2    Qiu, J.3
  • 14
    • 27944474776 scopus 로고    scopus 로고
    • ErmineJ: tool for functional analysis of gene expression data sets
    • H.K. Lee W. Braynen K. Keshav ErmineJ: tool for functional analysis of gene expression data sets BMC Bioinform 6 2005 269 276
    • (2005) BMC Bioinform , vol.6 , pp. 269-276
    • Lee, H.K.1    Braynen, W.2    Keshav, K.3
  • 15
    • 33646344978 scopus 로고    scopus 로고
    • STEM: a tool for the analysis of short time series gene expression data
    • J. Ernst Z. Bar-Joseph STEM: a tool for the analysis of short time series gene expression data BMC Bioinform 7 2006 191 201
    • (2006) BMC Bioinform , vol.7 , pp. 191-201
    • Ernst, J.1    Bar-Joseph, Z.2
  • 16
    • 12344257752 scopus 로고    scopus 로고
    • GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data
    • C.C. Wu H.C. Huang H.F. Juan GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data Bioinformatics 20 18 2004 3691 3693
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3691-3693
    • Wu, C.C.1    Huang, H.C.2    Juan, H.F.3
  • 17
    • 17044368752 scopus 로고    scopus 로고
    • Gene regulatory networks for development
    • M. Levine E.H. Davidson Gene regulatory networks for development Proc Natl Acad Sci USA 102 14 2005 4936 4942
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.14 , pp. 4936-4942
    • Levine, M.1    Davidson, E.H.2
  • 18
    • 34548538013 scopus 로고    scopus 로고
    • Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
    • F. Geier J. Timmer C. Fleck Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge BMC Syst Biol 1 2007 11 26
    • (2007) BMC Syst Biol , vol.1 , pp. 11-26
    • Geier, F.1    Timmer, J.2    Fleck, C.3
  • 19
    • 33746353952 scopus 로고    scopus 로고
    • Applying dynamic Bayesian networks to perturbed gene expression data
    • N. Dojer A. Gambin A. Mizera Applying dynamic Bayesian networks to perturbed gene expression data BMC Bioinform 7 2006 249 259
    • (2006) BMC Bioinform , vol.7 , pp. 249-259
    • Dojer, N.1    Gambin, A.2    Mizera, A.3
  • 20
    • 33750277449 scopus 로고    scopus 로고
    • Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A
    • T. Erkens M. Van Poucke J. Vandesompele Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A BMC Biotechnol 6 2006 41 48
    • (2006) BMC Biotechnol , vol.6 , pp. 41-48
    • Erkens, T.1    Van Poucke, M.2    Vandesompele, J.3
  • 21
    • 14844364789 scopus 로고    scopus 로고
    • Post-analysis follow-up and validation of microarray experiments
    • R.F. Chuaqui R.F. Bonner C.J. Best Post-analysis follow-up and validation of microarray experiments Nat Genet 32 Suppl. 2002 509 514
    • (2002) Nat Genet , vol.32 , Issue.Suppl. , pp. 509-514
    • Chuaqui, R.F.1    Bonner, R.F.2    Best, C.J.3
  • 22
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • J. Vandesompele K. De Preter F. Pattyn Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Genome Biol 3 7 2002 34 45
    • (2002) Genome Biol , vol.3 , Issue.7 , pp. 34-45
    • Vandesompele, J.1    De Preter, K.2    Pattyn, F.3
  • 23
    • 18744378860 scopus 로고    scopus 로고
    • Empirical Bayes screening of many P-values with applications to microarray studies
    • S. Datta S. Datta Empirical Bayes screening of many P -values with applications to microarray studies Bioinformatics 21 9 2005 1987 1994
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1987-1994
    • Datta, S.1    Datta, S.2
  • 24
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: from disarray to consolidation and consensus
    • D.B. Allison X. Cui G.P. Page Microarray data analysis: from disarray to consolidation and consensus Nat Rev Genet 7 1 2006 55 65
    • (2006) Nat Rev Genet , vol.7 , Issue.1 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3
  • 25
    • 33845913494 scopus 로고    scopus 로고
    • Estimating P-values in small microarray experiments
    • H. Yang G. Churchill Estimating P -values in small microarray experiments Bioinformatics 23 1 2007 38 43
    • (2007) Bioinformatics , vol.23 , Issue.1 , pp. 38-43
    • Yang, H.1    Churchill, G.2
  • 26
    • 34047257477 scopus 로고    scopus 로고
    • Protecting the cellular energy state during contractions: role of AMP deaminase
    • C.R. Hancock J.J. Brault R.L. Terjung Protecting the cellular energy state during contractions: role of AMP deaminase Physiol Pharmacol 57 Suppl. 10 2006 17 29
    • (2006) Physiol Pharmacol , vol.57 , Issue.Suppl. 10 , pp. 17-29
    • Hancock, C.R.1    Brault, J.J.2    Terjung, R.L.3
  • 27
    • 33750483907 scopus 로고    scopus 로고
    • Development of inosine monophosphate and its degradation products during aging of pork of different qualities in relation to basic taste and retronasal flavor perception of the meat
    • M. Tikk K. Tikk M.A. Tørngren Development of inosine monophosphate and its degradation products during aging of pork of different qualities in relation to basic taste and retronasal flavor perception of the meat J Agric Food Chem 54 20 2006 7769 7777
    • (2006) J Agric Food Chem , vol.54 , Issue.20 , pp. 7769-7777
    • Tikk, M.1    Tikk, K.2    Tørngren, M.A.3
  • 28
    • 0034048701 scopus 로고    scopus 로고
    • The porcine adenosine monophosphate deaminase 1 (AMPD1) gene maps to chromosome 4
    • A. Stratil A. Knoll G. Moser The porcine adenosine monophosphate deaminase 1 ( AMPD1 ) gene maps to chromosome 4 Anim Genet 31 2 2000 147 148
    • (2000) Anim Genet , vol.31 , Issue.2 , pp. 147-148
    • Stratil, A.1    Knoll, A.2    Moser, G.3
  • 29
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • M.B. Eisen P.T. Spellman P.O. Brown Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 95 25 1998 14863 14868
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3
  • 30
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • S. Tavazoie J.D. Hughes M.J. Campbell Systematic determination of genetic network architecture Nat Genet 22 3 1999 281 285
    • (1999) Nat Genet , vol.22 , Issue.3 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.D.2    Campbell, M.J.3
  • 31
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self organizing maps: methods and applications to hematopoietic differentiation
    • P. Tamayo D. Slonim J. Mesirov Interpreting patterns of gene expression with self organizing maps: methods and applications to hematopoietic differentiation Proc Natl Acad Sci USA 96 6 1999 2907 2912
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.6 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3
  • 32
    • 19544375816 scopus 로고    scopus 로고
    • The Graphical Query Language: a tool for analysis of gene expression time-courses
    • I.G. Costa A. Schönhuth A. Schliep The Graphical Query Language: a tool for analysis of gene expression time-courses Bioinformatics 21 10 2005 2544 2545
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2544-2545
    • Costa, I.G.1    Schönhuth, A.2    Schliep, A.3
  • 34
    • 28644452470 scopus 로고    scopus 로고
    • Clustering short time series gene expression data
    • J. Ernst G.J. Nau Z. Bar-Joseph Clustering short time series gene expression data Bioinformatics 21 Suppl. 1 2005 159 168
    • (2005) Bioinformatics , vol.21 , Issue.Suppl. 1 , pp. 159-168
    • Ernst, J.1    Nau, G.J.2    Bar-Joseph, Z.3
  • 35
    • 0033452362 scopus 로고    scopus 로고
    • Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes
    • M.G. Walker W. Volkmuth E. Sprinzak Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes Genome Res 9 12 1999 1198 1203
    • (1999) Genome Res , vol.9 , Issue.12 , pp. 1198-1203
    • Walker, M.G.1    Volkmuth, W.2    Sprinzak, E.3
  • 36
    • 0036940312 scopus 로고    scopus 로고
    • How well do we understand the clusters found in microarray data?
    • A. Clare R.D. King How well do we understand the clusters found in microarray data? In Silico Biol 2 4 2002 511 522
    • (2002) In Silico Biol , vol.2 , Issue.4 , pp. 511-522
    • Clare, A.1    King, R.D.2
  • 37
    • 0037053326 scopus 로고    scopus 로고
    • Peroxisome proliferator-activated receptor (PPAR) gamma coactivator-1 recruitment regulates PPAR subtype specificity
    • H. Oberkofler H. Esterbauer V. Linnemayr Peroxisome proliferator-activated receptor ( PPAR ) gamma coactivator-1 recruitment regulates PPAR subtype specificity J Biol Chem 277 19 2002 16750 16757
    • (2002) J Biol Chem , vol.277 , Issue.19 , pp. 16750-16757
    • Oberkofler, H.1    Esterbauer, H.2    Linnemayr, V.3
  • 38
    • 0033710665 scopus 로고    scopus 로고
    • Regulation of adipogenesis and energy balance by PPAR gamma and PGC-1
    • B.M. Spiegelman P. Puigserver Z. Wu Regulation of adipogenesis and energy balance by PPAR gamma and PGC-1 Int J Obes 24 Suppl. 4 2000 8 10
    • (2000) Int J Obes , vol.24 , Issue.Suppl. 4 , pp. 8-10
    • Spiegelman, B.M.1    Puigserver, P.2    Wu, Z.3
  • 39
    • 0033538473 scopus 로고    scopus 로고
    • Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1
    • Z. Wu P. Puigserver U. Andersson Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1 Cell 98 1 1999 115 124
    • (1999) Cell , vol.98 , Issue.1 , pp. 115-124
    • Wu, Z.1    Puigserver, P.2    Andersson, U.3
  • 40
    • 0035855858 scopus 로고    scopus 로고
    • Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1
    • J.C. Yoon P. Puigserver G. Chen Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1 Nature 413 6852 2001 131 138
    • (2001) Nature , vol.413 , Issue.6852 , pp. 131-138
    • Yoon, J.C.1    Puigserver, P.2    Chen, G.3
  • 41
    • 0032549811 scopus 로고    scopus 로고
    • A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis
    • P. Puigserver Z. Wu C.W. Park A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis Cell 92 6 1998 829 839
    • (1998) Cell , vol.92 , Issue.6 , pp. 829-839
    • Puigserver, P.1    Wu, Z.2    Park, C.W.3
  • 42
    • 0037102256 scopus 로고    scopus 로고
    • Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres
    • J. Lin H. Wu P.T. Tarr Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres Nature 418 6899 2002 797 801
    • (2002) Nature , vol.418 , Issue.6899 , pp. 797-801
    • Lin, J.1    Wu, H.2    Tarr, P.T.3
  • 43
    • 0035957375 scopus 로고    scopus 로고
    • Restoration of insulin-sensitive glucose transporter (GLUT4) gene expression in muscle cells by the transcriptional coactivator PGC-1
    • L.F. Michael Z. Wu R.B. Cheatham Restoration of insulin-sensitive glucose transporter ( GLUT4 ) gene expression in muscle cells by the transcriptional coactivator PGC-1 Proc Natl Acad Sci USA 98 7 2001 3820 3825
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.7 , pp. 3820-3825
    • Michael, L.F.1    Wu, Z.2    Cheatham, R.B.3
  • 44
    • 27644490342 scopus 로고    scopus 로고
    • Porcine PPARGC1A (peroxisome proliferative activated receptor gamma coactivator 1A): coding sequence, genomic organization, polymorphisms and mapping
    • K. Jacobs G. Rohrer M. Van Poucke Porcine PPARGC1A (peroxisome proliferative activated receptor gamma coactivator 1A): coding sequence, genomic organization, polymorphisms and mapping Cytogenet Genome Res 112 1–2 2006 106 113
    • (2006) Cytogenet Genome Res , vol.112 , Issue.1–2 , pp. 106-113
    • Jacobs, K.1    Rohrer, G.2    Van Poucke, M.3
  • 45
    • 0038686576 scopus 로고    scopus 로고
    • Suppression of beta cell energy metabolism and insulin release by PGC-1 alpha
    • J.C. Yoon G. Xu J.T. Deeney Suppression of beta cell energy metabolism and insulin release by PGC-1 alpha Dev Cell 5 1 2003 73 83
    • (2003) Dev Cell , vol.5 , Issue.1 , pp. 73-83
    • Yoon, J.C.1    Xu, G.2    Deeney, J.T.3
  • 46
    • 23444460778 scopus 로고    scopus 로고
    • Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
    • R. Wernersson M.H. Schierup F.G. Jørgensen Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing BMC Genomics 6 1 2005 70 77
    • (2005) BMC Genomics , vol.6 , Issue.1 , pp. 70-77
    • Wernersson, R.1    Schierup, M.H.2    Jørgensen, F.G.3
  • 47
    • 33846813359 scopus 로고    scopus 로고
    • Uncoupling protein-3: clues in an ongoing mitochondrial mystery
    • V. Bézaire E.L. Seifert M.E. Harper Uncoupling protein-3: clues in an ongoing mitochondrial mystery FASEB J 21 2 2007 312 324
    • (2007) FASEB J , vol.21 , Issue.2 , pp. 312-324
    • Bézaire, V.1    Seifert, E.L.2    Harper, M.E.3
  • 48
    • 0033809963 scopus 로고    scopus 로고
    • Isolation and assignment of the UDP-glucose pyrophosphorylase gene (UGP2) to porcine chromosome 3q21→q22 by FISH and by analysis of somatic cell and radiation hybrid panels
    • C. Looft S. Paul P.D. Thomsen Isolation and assignment of the UDP-glucose pyrophosphorylase gene ( UGP2 ) to porcine chromosome 3q21 → q22 by FISH and by analysis of somatic cell and radiation hybrid panels Cytogenet Cell Genet 89 3–4 2000 154 155
    • (2000) Cytogenet Cell Genet , vol.89 , Issue.3–4 , pp. 154-155
    • Looft, C.1    Paul, S.2    Thomsen, P.D.3
  • 49
    • 32144437945 scopus 로고    scopus 로고
    • Evaluation of methods for oligonucleotide array data via quantitative real-time PCR
    • L.X. Qin R.P. Beyer F.N. Hudson Evaluation of methods for oligonucleotide array data via quantitative real-time PCR BMC Bioinform 7 2006 23 34
    • (2006) BMC Bioinform , vol.7 , pp. 23-34
    • Qin, L.X.1    Beyer, R.P.2    Hudson, F.N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.