Inferring the in vivo cellular program of developing bovine skeletal muscle from expression data

Gene Expression Patterns

Volumn 13, Issue 3-4, 2013, Pages 109-125

  Hudson, Nicholas J ^a   Lyons, Russell E ^a   Reverter, Antonio ^a   Greenwood, Paul L ^b   Dalrymple, Brian P ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF NEW ENGLAND   (Australia)

Author keywords

Epigenetic; Mitochondria; Muscle development; Transcription factors

Indexed keywords

AGXT2L1 PROTEIN; CKMT2 PROTEIN; MYOGENIC FACTOR 5; MYOSIN SUBFRAGMENT; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA COACTIVATOR 1ALPHA; PROTEIN; PYRUVATE DEHYDROGENASE KINASE 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DACH2; TRANSCRIPTION FACTOR EYA2; TRANSCRIPTION FACTOR HES6; TRANSCRIPTION FACTOR MYF6; TRANSCRIPTION FACTOR MYOG; TRANSCRIPTION FACTOR PAX7; TRANSCRIPTION FACTOR SIX1; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG; UNCOUPLING PROTEIN 3;

ARTICLE; DOWN REGULATION; HUMAN; IN VIVO STUDY; MUSCLE DEVELOPMENT; MUSCLE MASS; MUSCLE METABOLISM; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; SKELETAL MUSCLE;

ANIMALS; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CATTLE; CELL DIFFERENTIATION; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; MICE; MITOCHONDRIA, MUSCLE; MUSCLE DEVELOPMENT; MUSCLE, SKELETAL; MYOGENIC REGULATORY FACTOR 5; MYOGENIN; PAX7 TRANSCRIPTION FACTOR; REPRESSOR PROTEINS; TRANSCRIPTION FACTORS;

EID: 84874841286     PISSN: 1567133X     EISSN: 18727298     Source Type: Journal    
DOI: 10.1016/j.gep.2013.02.001     Document Type: Article

References (97)

1. A. Almenar-Queralt, A. Lee, C.A. Conley, L. Ribas de Pouplana, and V.M. Fowler Identification of a novel tropomodulin isoform, skeletal tropomodulin, that caps actin filament pointed ends in fast skeletal muscle J. Biol. Chem. 274 1999 28466 28475
2. A. Bafico, A. Gazit, T. Pramila, P.W. Finch, A. Yaniv, and S.A. Aaronson Interaction of frizzled related protein (FRP) with Wnt ligands and the frizzled receptor suggests alternative mechanisms for FRP inhibition of Wnt signaling J. Biol. Chem. 274 1999 16180 16187
3. J.R. Beauchamp, L. Heslop, D.S. Yu, S. Tajbakhsh, R.G. Kelly, A. Wernig, M.E. Buckingham, T.A. Partridge, and P.S. Zammit Expression of CD34 and Myf5 defines the majority of quiescent adult skeletal muscle satellite cells J. Cell Biol. 151 2000 1221 1234
4. A.W. Bell Lipid metabolism in liver and selected tissues and in the whole body of ruminant animals Prog. Lipid Res. 18 1979 117 164
5. I.H. Bellayr, X. Mu, and Y. Li Biochemical insights into the role of matrix metalloproteinases in regeneration: challenges and recent developments Future Med. Chem. 1 2009 1095 1111
6. C. Berry, M. Thomas, B. Langley, M. Sharma, and R. Kambadur Single cysteine to tyrosine transition inactivates the growth inhibitory function of Piedmontese myostatin Am. J. Physiol. Cell Physiol. 283 2002 C135 C141
7. S. Bicer, and P.J. Reiser Myosin light chain isoform expression among single mammalian skeletal muscle fibers: species variations J. Mus. Res. Cell Motil. 25 2004 623 633 (Pubitemid 40562028)
8. S. Biressi, E. Tagliafico, G. Lamorte, S. Monteverde, E. Tenedini, E. Roncaglia, S. Ferrari, M.G. Cusella-De Angelis, S. Tajbakhsh, and G. Cossu Intrinsic phenotypic diversity of embryonic and fetal myoblasts is revealed by genome-wide gene expression analysis on purified cells Dev. Biol. 304 2007 633 651 (Pubitemid 46546388)
9. M. Bonnet, I. Cassar-Malek, Y. Chilliard, and B. Picard Ontogenesis of muscle and adipose tissues and their interactions in ruminants and other species Animal 4 2010 1093 1109
10. R. Bottinelli, and C. Reggiani Human skeletal muscle fibres: molecular and functional diversity Prog. Biophys. Mol. Biol. 73 2000 195 262
11. J.M. Boucher, S.M. Peterson, S. Urs, C. Zhang, and L. Liaw The miR-143/145 cluster is a novel transcriptional target of Jagged-1/Notch signaling in vascular smooth muscle cells J. Biol. Chem. 286 2011 28312 28321
12. B. Brunmair, K. Staniek, J. Dorig, Z. Szocs, K. Stadlbauer, V. Marian, F. Gras, C. Anderwald, H. Nohl, W. Waldhausl, and C. Furnsinn Activation of PPAR-delta in isolated rat skeletal muscle switches fuel preference from glucose to fatty acids Diabetologia 49 2006 2713 2722
13. M. Buckingham Skeletal muscle formation in vertebrates Curr. Opin. Genet. Dev. 11 2001 440 448 (Pubitemid 32614204)
14. K. Byrne, T. Vuocolo, C. Gondro, J.D. White, N.E. Cockett, T. Hadfield, C.A. Bidwell, J.N. Waddell, and R.L. Tellam A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development BMC Genom. 11 2010 378
15. F. Chemello, C. Bean, P. Cancellara, P. Laveder, C. Reggiani, and G. Lanfranchi Microgenomic analysis in skeletal muscle: expression signatures of individual fast and slow myofibers PLoS One 6 2011 e16807
16. W. Chen, X. Zhang, K. Birsoy, and R.G. Roeder A muscle-specific knockout implicates nuclear receptor coactivator MED1 in the regulation of glucose and energy metabolism Proc. Natl. Acad. Sci. U.S.A. 107 2010 10196 10201
17. C. Conte, N. Ainaoui, A. Delluc-Clavieres, M.P. Khoury, R. Azar, F. Pujol, Y. Martineau, S. Pyronnet, and A.C. Prats Fibroblast growth factor 1 induced during myogenesis by a transcription-translation coupling mechanism Nucleic Acids Res. 37 2009 5267 5278
18. P. Cronje Ruminant Physiology: Digestion, Metabolism, Growth and Reproduction 2000 CABI Publishing Oxon, UK
19. N. De Jager, N.J. Hudson, A. Reverter, Y.H. Wang, S.H. Nagaraj, L.M. Cafe, P.L. Greenwood, R.T. Barnard, K.P. Kongsuwan, and B.P. Dalrymple Chronic exposure to anabolic steroids induces the muscle expression of oxytocin and a more than fiftyfold increase in circulating oxytocin in cattle Physiol. Genom. 43 2011 467 478
20. J. de Wilde, M.F. Hulshof, M.V. Boekschoten, P. de Groot, E. Smit, and E.C. Mariman The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way BMC Genom. 11 2010 176
21. M. Deries, J.J. Collins, and M.J. Duxson The mammalian myotome: a muscle with no innervation Evol. Dev. 10 2008 746 755
22. J. Diamond Evolution, consequences and future of plant and animal domestication Nature 418 2002 700 707
23. T. Dupas, T. Rouaud, K. Rouger, B. Lieubeau, C. Cario-Toumaniantz, J. Fontaine-Perus, M.F. Gardahaut, and G. Auda-Boucher Fetal muscle contains different CD34+ cell subsets that distinctly differentiate into adipogenic, angiogenic and myogenic lineages Stem Cell Res. 7 2011 230 243
24. C.G. Elsik, R.L. Tellam, K.C. Worley, R.A. Gibbs, D.M. Muzny, G.M. Weinstock, D.L. Adelson, E.E. Eichler, L. Elnitski, R. Guigo, D.L. Hamernik, S.M. Kappes, H.A. Lewin, D.J. Lynn, F.W. Nicholas, A. Reymond, M. Rijnkels, L.C. Skow, E.M. Zdobnov, L. Schook, J. Womack, T. Alioto, S.E. Antonarakis, A. Astashyn, C.E. Chapple, H.C. Chen, J. Chrast, F. Camara, O. Ermolaeva, C.N. Henrichsen, W. Hlavina, Y. Kapustin, B. Kiryutin, P. Kitts, F. Kokocinski, M. Landrum, D. Maglott, K. Pruitt, V. Sapojnikov, S.M. Searle, V. Solovyev, A. Souvorov, C. Ucla, C. Wyss, J.M. Anzola, D. Gerlach, E. Elhaik, D. Graur, J.T. Reese, R.C. Edgar, J.C. McEwan, G.M. Payne, J.M. Raison, T. Junier, E.V. Kriventseva, E. Eyras, M. Plass, R. Donthu, D.M. Larkin, J. Reecy, M.Q. Yang, L. Chen, Z. Cheng, C.G. Chitko-McKown, G.E. Liu, L.K. Matukumalli, J. Song, B. Zhu, D.G. Bradley, F.S. Brinkman, L.P. Lau, M.D. Whiteside, A. Walker, T.T. Wheeler, T. Casey, J.B. German, D.G. Lemay, N.J. Maqbool, A.J. Molenaar, S. Seo, P. Stothard, C.L. Baldwin, R. Baxter, C.L. Brinkmeyer-Langford, W.C. Brown, C.P. Childers, T. Connelley, S.A. Ellis, K. Fritz, E.J. Glass, C.T. Herzig, A. Iivanainen, K.K. Lahmers, A.K. Bennett, C.M. Dickens, J.G. Gilbert, D.E. Hagen, H. Salih, J. Aerts, A.R. Caetano, B. Dalrymple, J.F. Garcia, C.A. Gill, S.G. Hiendleder, E. Memili, D. Spurlock, J.L. Williams, L. Alexander, M.J. Brownstein, L. Guan, R.A. Holt, S.J. Jones, M.A. Marra, R. Moore, S.S. Moore, A. Roberts, M. Taniguchi, R.C. Waterman, J. Chacko, M.M. Chandrabose, A. Cree, M.D. Dao, H.H. Dinh, R.A. Gabisi, S. Hines, J. Hume, S.N. Jhangiani, V. Joshi, C.L. Kovar, L.R. Lewis, Y.S. Liu, J. Lopez, M.B. Morgan, N.B. Nguyen, G.O. Okwuonu, S.J. Ruiz, J. Santibanez, R.A. Wright, C. Buhay, Y. Ding, S. Dugan-Rocha, J. Herdandez, M. Holder, A. Sabo, A. Egan, J. Goodell, K. Wilczek-Boney, G.R. Fowler, M.E. Hitchens, R.J. Lozado, C. Moen, D. Steffen, J.T. Warren, J. Zhang, R. Chiu, J.E. Schein, K.J. Durbin, P. Havlak, H. Jiang, Y. Liu, X. Qin, Y. Ren, Y. Shen, H. Song, S.N. Bell, C. Davis, A.J. Johnson, S. Lee, L.V. Nazareth, B.M. Patel, L.L. Pu, S. Vattathil, R.L. Williams Jr., S. Curry, C. Hamilton, E. Sodergren, D.A. Wheeler, W. Barris, G.L. Bennett, A. Eggen, R.D. Green, G.P. Harhay, M. Hobbs, O. Jann, J.W. Keele, M.P. Kent, S. Lien, S.D. McKay, S. McWilliam, A. Ratnakumar, R.D. Schnabel, T. Smith, W.M. Snelling, T.S. Sonstegard, R.T. Stone, Y. Sugimoto, A. Takasuga, J.F. Taylor, C.P. Van Tassell, M.D. Macneil, A.R. Abatepaulo, C.A. Abbey, V. Ahola, I.G. Almeida, A.F. Amadio, E. Anatriello, S.M. Bahadue, F.H. Biase, C.R. Boldt, J.A. Carroll, W.A. Carvalho, E.P. Cervelatti, E. Chacko, J.E. Chapin, Y. Cheng, J. Choi, A.J. Colley, T.A. de Campos, M. De Donato, I.K. Santos, C.J. de Oliveira, H. Deobald, E. Devinoy, K.E. Donohue, P. Dovc, A. Eberlein, C.J. Fitzsimmons, A.M. Franzin, G.R. Garcia, S. Genini, C.J. Gladney, J.R. Grant, M.L. Greaser, J.A. Green, D.L. Hadsell, H.A. Hakimov, R. Halgren, J.L. Harrow, E.A. Hart, N. Hastings, M. Hernandez, Z.L. Hu, A. Ingham, T. Iso-Touru, C. Jamis, K. Jensen, D. Kapetis, T. Kerr, S.S. Khalil, H. Khatib, D. Kolbehdari, C.G. Kumar, D. Kumar, R. Leach, J.C. Lee, C. Li, K.M. Logan, R. Malinverni, E. Marques, W.F. Martin, N.F. Martins, S.R. Maruyama, R. Mazza, K.L. McLean, J.F. Medrano, B.T. Moreno, D.D. More, C.T. Muntean, H.P. Nandakumar, M.F. Nogueira, I. Olsaker, S.D. Pant, F. Panzitta, R.C. Pastor, M.A. Poli, N. Poslusny, S. Rachagani, S. Ranganathan, A. Razpet, P.K. Riggs, G. Rincon, N. Rodriguez-Osorio, S.L. Rodriguez-Zas, N.E. Romero, A. Rosenwald, L. Sando, S.M. Schmutz, L. Shen, L. Sherman, B.R. Southey, Y.S. Lutzow, J.V. Sweedler, I. Tammen, B.P. Telugu, J.M. Urbanski, Y.T. Utsunomiya, C.P. Verschoor, A.J. Waardenberg, Z. Wang, R. Ward, R. Weikard, T.H. Welsh Jr., S.N. White, L.G. Wilming, K.R. Wunderlich, J. Yang, and F.Q. Zhao The genome sequence of taurine cattle: a window to ruminant biology and evolution Science 324 2009 522 528
25. D.I. Finkelstein, P. Andrianakis, A.R. Luff, and D. Walker Effects of thyroidectomy on development of skeletal muscle in fetal sheep Am. J. Physiol. 261 1991 R1300 R1306
26. A. Fritah Control of skeletal muscle metabolic properties by the nuclear receptor corepressor RIP140 Appl. Physiol. Nutr. Metab. 34 2009 362 367
27. X.M. Gao, T. Chandra, M.O. Gratton, I. Quelo, J. Prud'homme, S. Stifani, and R. St-Arnaud HES6 acts as a transcriptional repressor in myoblasts and can induce the myogenic differentiation program J. Cell Biol. 154 2001 1161 1171 (Pubitemid 34286194)
28. N. Gleyzer, K. Vercauteren, and R.C. Scarpulla Control of mitochondrial transcription specificity factors (TFB1M and TFB2M) by nuclear respiratory factors (NRF-1 and NRF-2) and PGC-1 family coactivators Mol. Cell. Biol. 25 2005 1354 1366 (Pubitemid 40204913)
29. D. Gospodarowicz, J. Weseman, J.S. Moran, and J. Lindstrom Effect of fibroblast growth factor on the division and fusion of bovine myoblasts J. Cell Biol. 70 1976 395 405
30. P.L. Greenwood, and L.M. Cafe Prenatal and pre-weaning growth and nutrition of cattle: longterm consequences for beef production Animal 1 2007 1283 1296 (Pubitemid 47519277)
31. P.L. Greenwood, R.M. Slepetis, J.W. Hermanson, and A.W. Bell Intrauterine growth retardation is associated with reduced cell cycle activity, but not myofibre number, in ovine fetal muscle Reprod. Fertil. Dev. 11 1999 281 291
32. M. Haldar, G. Karan, P. Tvrdik, and M.R. Capecchi Two cell lineages, myf5 and myf5-independent, participate in mouse skeletal myogenesis Dev. Cell 14 2008 437 445
33. K. Havstad, and J. Malechek Energy expenditure by heifers grazing crested wheatgrass of diminishing availability J. Range Manage. 35 1982 447 450
34. T.A. Heanue, R. Reshef, R.J. Davis, G. Mardon, G. Oliver, S. Tomarev, A.B. Lassar, and C.J. Tabin Synergistic regulation of vertebrate muscle development by Dach2, Eya2, and Six1, homologs of genes required for Drosophila eye formation Genes Dev. 13 1999 3231 3243 (Pubitemid 30030445)
35. H. Hoppeler, and M. Fluck Normal mammalian skeletal muscle and its phenotypic plasticity J. Exp. Biol. 205 2002 2143 2152
36. N.J. Hudson Symmorphosis and livestock bioenergetics: production animal muscle has low mitochondrial volume fractions J. Anim. Physiol. Anim. Nutr. (Berl) 93 2009 1 6
37. N.J. Hudson, A. Reverter, and B.P. Dalrymple A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation PLoS Comput. Biol. 5 2009 e1000382
38. N.J. Hudson, A. Reverter, Y. Wang, P.L. Greenwood, and B.P. Dalrymple Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks PLoS One 4 2009 e7249
39. R. Hunter Hormonal growth promotant (HGP) use in the Australian beef industry Anim. Prod. Sci. 50 2010 637 659
40. L. Hutley, W. Shurety, F. Newell, R. McGeary, N. Pelton, J. Grant, A. Herington, D. Cameron, J. Whitehead, and J. Prins Fibroblast growth factor 1: a key regulator of human adipogenesis Diabetes 53 2004 3097 3106 (Pubitemid 39564484)
41. Y. Izumiya, T. Hopkins, C. Morris, K. Sato, L. Zeng, J. Viereck, J.A. Hamilton, N. Ouchi, N.K. LeBrasseur, and K. Walsh Fast/Glycolytic muscle fiber growth reduces fat mass and improves metabolic parameters in obese mice Cell Metab. 7 2008 159 172 (Pubitemid 351168553)
42. D. Joulia, H. Bernardi, V. Garandel, F. Rabenoelina, B. Vernus, and G. Cabello Mechanisms involved in the inhibition of myoblast proliferation and differentiation by myostatin Exp. Cell Res. 286 2003 263 275 (Pubitemid 36566439)
43. K.A. Kennedy, T. Porter, V. Mehta, S.D. Ryan, F. Price, V. Peshdary, C. Karamboulas, J. Savage, T.A. Drysdale, S.C. Li, S.A. Bennett, and I.S. Skerjanc Retinoic acid enhances skeletal muscle progenitor formation and bypasses inhibition by bone morphogenetic protein 4 but not dominant negative beta-catenin BMC Biol. 7 2009 67
44. H. Kiaris, I. Chatzistamou, A.G. Papavassiliou, and A.V. Schally Growth hormone-releasing hormone: not only a neurohormone Trends Endocrinol. Metab. 22 2011 311 317
45. H. Kudo, N. Amizuka, K. Araki, K. Inohaya, and A. Kudo Zebrafish periostin is required for the adhesion of muscle fiber bundles to the myoseptum and for the differentiation of muscle fibers Dev. Biol. 267 2004 473 487 (Pubitemid 38328586)
46. P. Lafuste, C. Sonnet, B. Chazaud, P.A. Dreyfus, R.K. Gherardi, U.M. Wewer, and F.J. Authier ADAM12 and alpha9beta1 integrin are instrumental in human myogenic cell differentiation Mol. Biol. Cell 16 2005 861 870 (Pubitemid 40165577)
47. L. Larsson, X. Li, A. Teresi, and G. Salviati Effects of thyroid hormone on fast- and slow-twitch skeletal muscles in young and old rats J. Physiol. 481 Pt. 1 1994 149 161 (Pubitemid 24361355)
48. S.J. Lee Quadrupling muscle mass in mice by targeting TGF-beta signaling pathways PLoS One 2 2007 e789
49. S.A. Lehnert, A. Reverter, K.A. Byrne, Y. Wang, G.S. Nattrass, N.J. Hudson, and P.L. Greenwood Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds BMC Dev. Biol. 7 2007 95
50. J. Lin, H. Wu, P.T. Tarr, C.Y. Zhang, Z. Wu, O. Boss, L.F. Michael, P. Puigserver, E. Isotani, E.N. Olson, B.B. Lowell, R. Bassel-Duby, and B.M. Spiegelman Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres Nature 418 2002 797 801
51. X. Liu, X. Yu, D.J. Zack, H. Zhu, and J. Qian TiGER: a database for tissue-specific gene expression and regulation BMC Bioinformatics 9 2008 271
52. M. Lockhart, E. Wirrig, A. Phelps, and A. Wessels Extracellular matrix and heart development Birth Defects Res. A Clin. Mol. Teratol. 91 2011 535 550
53. M. Mariasegaram, A. Reverter, W. Barris, S.A. Lehnert, B. Dalrymple, and K. Prayaga Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle BMC Genom. 11 2010 370
54. A. McDermott, M. Gustafsson, T. Elsam, C.C. Hui, C.P. Emerson Jr., and A.G. Borycki Gli2 and Gli3 have redundant and context-dependent function in skeletal muscle formation Development 132 2005 345 357 (Pubitemid 40268284)
55. R. Meech, M. Gomez, C. Woolley, M. Barro, J.A. Hulin, E.C. Walcott, J. Delgado, and H.P. Makarenkova The Homeobox transcription factor Barx2 regulates plasticity of young primary myofibers PloS One 5 2010
56. J.B. Miller, L. Schaefer, and J.A. Dominov Seeking muscle stem cells Curr. Top. Dev. Biol. 43 1999 191 219
57. J.L. Moran, Y. Li, A.A. Hill, W.M. Mounts, and C.P. Miller Gene expression changes during mouse skeletal myoblast differentiation revealed by transcriptional profiling Physiol. Genom. 10 2002 103 111 (Pubitemid 135707434)
58. P.Y. Muller, H. Janovjak, A.R. Miserez, and Z. Dobbie Processing of gene expression data generated by quantitative real-time RT-PCR Biotechniques 32 2002 1372 1374 1376, 1378-1379
59. C. Niehrs Function and biological roles of the Dickkopf family of Wnt modulators Oncogene 25 2006 7469 7481 (Pubitemid 44885746)
60. F.C. Nielsen, J. Nielsen, and J. Christiansen A family of IGF-II mRNA binding proteins (IMP) involved in RNA trafficking Scand. J. Clin. Lab. Invest. Suppl. 234 2001 93 99 (Pubitemid 33043632)
61. N. Novac, and T. Heinzel Nuclear receptors: overview and classification Curr. Drug Targets Inflamm. Allergy 3 2004 335 346 (Pubitemid 39534770)
62. T. Partridge Developmental biology: skeletal muscle comes of age Nature 460 2009 584 585
63. M.A. Pearen, and G.E. Muscat Minireview: nuclear hormone receptor 4A signaling: implications for metabolic disease Mol. Endocrinol. 24 2010 1891 1903
64. H. Petropoulos, P.J. Gianakopoulos, A.G. Ridgeway, and I.S. Skerjanc Disruption of Meox or Gli activity ablates skeletal myogenesis in P19 cells J. Biol. Chem. 279 2004 23874 23881 (Pubitemid 38725244)
65. H. Petropoulos, and I.S. Skerjanc Beta-catenin is essential and sufficient for skeletal myogenesis in P19 cells J. Biol. Chem. 277 2002 15393 15399 (Pubitemid 34967801)
66. B. Picard, L. Lefaucheur, C. Berri, and M.J. Duclos Muscle fibre ontogenesis in farm animal species Reprod. Nutr. Dev. 42 2002 415 431 (Pubitemid 36113384)
67. T.P. Rao, and M. Kuhl An updated overview on Wnt signaling pathways: a prelude for more Circ. Res. 106 2010 1798 1806
68. A. Reverter, W. Barris, S. McWilliam, K.A. Byrne, Y.H. Wang, S.H. Tan, N. Hudson, and B.P. Dalrymple Validation of alternative methods of data normalization in gene co-expression studies Bioinformatics 21 2005 1112 1120 (Pubitemid 40467935)
69. A. Reverter, N.J. Hudson, S.H. Nagaraj, M. Perez-Enciso, and B.P. Dalrymple Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data Bioinformatics 26 2010 896 904
70. P.C. Rida, N. Le Minh, and Y.J. Jiang A Notch feeling of somite segmentation and beyond Dev. Biol. 265 2004 2 22 (Pubitemid 38018818)
71. A.G. Ridgeway, and I.S. Skerjanc Pax3 is essential for skeletal myogenesis and the expression of Six1 and Eya2 J. Biol. Chem. 276 2001 19033 19039
72. D.J. Robbins, D.L. Fei, and N.A. Riobo The hedgehog signal transduction network Sci. Signal. 5 2012 re6
73. R.G. Russell, and F.T. Oteruelo An ultrastructural study of the differentiation of skeletal muscle in the bovine fetus Anat. Embryol. (Berl) 162 1981 403 417 (Pubitemid 11060016)
74. S. Schiaffino, and C. Mammucari Regulation of skeletal muscle growth by the IGF1-Akt/PKB pathway: insights from genetic models Skelet. Muscle 1 2011 4
75. K. Schmidt, G. Glaser, A. Wernig, M. Wegner, and O. Rosorius Sox8 is a specific marker for muscle satellite cells and inhibits myogenesis J. Biol. Chem. 278 2003 29769 29775 (Pubitemid 36962363)
76. A. Seth, J.H. Steel, D. Nichol, V. Pocock, M.K. Kumaran, A. Fritah, M. Mobberley, T.A. Ryder, A. Rowlerson, J. Scott, M. Poutanen, R. White, and M. Parker The transcriptional corepressor RIP140 regulates oxidative metabolism in skeletal muscle Cell Metab. 6 2007 236 245 (Pubitemid 47324141)
77. M. Sheffield-Moore, and R.J. Urban An overview of the endocrinology of skeletal muscle Trends Endocrinol. Metab. 15 2004 110 115 (Pubitemid 38445064)
78. W.E. Stansfield, N.M. Andersen, R.H. Tang, and C.H. Selzman Periostin is a novel factor in cardiac remodeling after experimental and clinical unloading of the failing heart Ann. Thorac. Surg. 88 2009 1916 1921
79. C.A. Steelman, J.C. Recknor, D. Nettleton, and J.M. Reecy Transcriptional profiling of myostatin-knockout mice implicates Wnt signaling in postnatal skeletal muscle growth and hypertrophy FASEB J. 20 2006 580 582 (Pubitemid 46671256)
80. Suhaimi, A.H.M.S., 2009. Relationships between hypothalamic gene expression and the resumption of ovulation in postpartum beef cows, School of Animal Studies. University of Queensland, St. Lucia.
81. W.E. Taylor, S. Bhasin, J. Artaza, F. Byhower, M. Azam, D.H. Willard Jr., F.C. Kull Jr., and N. Gonzalez-Cadavid Myostatin inhibits cell proliferation and protein synthesis in C2C12 muscle cells Am. J. Physiol. Endocrinol. Metab. 280 2001 E221 E228
82. K. Uchiyama, A. Ishikawa, and K. Hanaoka Expression of lbx1 involved in the hypaxial musculature formation of the mouse embryo J. Exp. Zool. 286 2000 270 279 (Pubitemid 30096126)
83. R.J. Urban Growth hormone and testosterone: anabolic effects on muscle Horm. Res. Paediatr. 76 Suppl. 1 2011 81 83
84. J.H. van Weerd, K. Koshiba-Takeuchi, C. Kwon, and J.K. Takeuchi Epigenetic factors and cardiac development Cardiovasc. Res. 91 2011 203 211
85. T. Vaughan, J. Ryan, and N. Czaplewski Mammalogy 1999 Brooks Cole
86. J.A. Villena, M.B. Hock, W.Y. Chang, J.E. Barcas, V. Giguere, and A. Kralli Orphan nuclear receptor estrogen-related receptor alpha is essential for adaptive thermogenesis Proc. Natl. Acad. Sci. U.S.A. 104 2007 1418 1423 (Pubitemid 46184019)
87. T. Vuocolo, K. Byrne, J. White, S. McWilliam, A. Reverter, N.E. Cockett, and R.L. Tellam Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle Physiol. Genom. 28 2007 253 272 (Pubitemid 46711003)
88. Y. Wang, A. Reverter, S.H. Tan, N. De Jager, R. Wang, S.M. McWilliam, L.M. Cafe, P.L. Greenwood, and S.A. Lehnert Gene expression patterns during intramuscular fat development in cattle J. Anim. Sci. 87 2008 119 130
89. Y.H. Wang, S.M. McWilliam, W. Barendse, S.R. Kata, J.E. Womack, S.S. Moore, and S.A. Lehnert Mapping of 12 bovine ribosomal protein genes using a bovine radiation hybrid panel Anim. Genet. 32 2001 269 273 (Pubitemid 33011519)
90. Y.X. Wang, C.L. Zhang, R.T. Yu, H.K. Cho, M.C. Nelson, C.R. Bayuga-Ocampo, J. Ham, H. Kang, and R.M. Evans Regulation of muscle fiber type and running endurance by PPARbdelta PLoS Biol. 2 2004 e294
91. E.R. Weibel, C.R. Taylor, and H. Hoppeler The concept of symmorphosis: a testable hypothesis of structure-function relationship Proc Natl Acad Sci U S A 88 1991 10357 10361 (Pubitemid 21915834)
92. H. Weintraub, S.J. Tapscott, R.L. Davis, M.J. Thayer, M.A. Adam, A.B. Lassar, and A.D. Miller Activation of muscle-specific genes in pigment, nerve, fat, liver, and fibroblast cell lines by forced expression of MyoD Proc. Natl. Acad. Sci. U.S.A. 86 1989 5434 5438 (Pubitemid 19185563)
93. B.A. Williams, and C.P. Ordahl Pax-3 expression in segmental mesoderm marks early stages in myogenic cell specification Development 120 1994 785 796 (Pubitemid 24111544)
94. M. Yamamoto, Y. Gotoh, K. Tamura, M. Tanaka, A. Kawakami, H. Ide, and A. Kuroiwa Coordinated expression of Hoxa-11 and Hoxa-13 during limb muscle patterning Development 125 1998 1325 1335 (Pubitemid 28203947)
95. M. Yamamoto, and A. Kuroiwa Hoxa-11 and Hoxa-13 are involved in repression of MyoD during limb muscle development Dev. Growth Differ. 45 2003 485 498 (Pubitemid 38067914)
96. C.C. Yang, H. Liu, S.L. Chen, T.H. Wang, C.L. Hsieh, Y. Huang, S.J. Chen, H.C. Chen, B.Y. Yung, and B. Chin-Ming Tan Epigenetic silencing of myogenic gene program by Myb-binding protein 1a suppresses myogenesis EMBO J. 31 2012 1739 1751
97. P.S. Zammit, T.A. Partridge, and Z. Yablonka-Reuveni The skeletal muscle satellite cell: the stem cell that came in from the cold J. Histochem. Cytochem. 54 2006 1177 1191 (Pubitemid 44623339)