Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Hudson, Nicholas J ^a   Reverter, Antonio ^a   Wang, Yong Hong ^a   Greenwood, Paul L ^b   Dalrymple, Brian P ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF NEW ENGLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

INTERFERON REGULATORY FACTOR 1; PROTEIN HLF; PROTEIN INHIBITOR OF ACTIVATED STAT; PROTEIN TFB2M; PROTEIN TLX3; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR SOX17; UNCLASSIFIED DRUG; OLIGONUCLEOTIDE;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; COW; GENE EXPRESSION; GENE FUNCTION; GENETIC ALGORITHM; MUSCLE DEVELOPMENT; NONHUMAN; PERINATAL PERIOD; SKELETAL MUSCLE; TRANSCRIPTION REGULATION; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; BIOPSY; CATTLE; CHEMISTRY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; METABOLISM; MITOCHONDRION; MUSCLE CONTRACTION;

BOS; BOVINAE;

ALGORITHMS; ANIMALS; BIOPSY; CATTLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; MITOCHONDRIA; MODELS, BIOLOGICAL; MUSCLE CONTRACTION; MUSCLE, SKELETAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; TRANSCRIPTION, GENETIC;

EID: 70349668879     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007249     Document Type: Article

References (90)

1. Takebe A, Era T, Okada M, Martin Jakt L, Kuroda Y, et al. (2006) Microarray analysis of PDGFR alpha+ populations in ES cell differentiation culture identifies genes involved in differentiation of mesoderm and mesenchyme including ARID3b that is essential for development of embryonic mesenchymal cells. Dev Biol 293: 25-37.
2. Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, et al. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452: 840-845.
3. Tuch BB, Li H, Johnson AD (2008) Evolution of eukaryotic transcription circuits. Science 319: 1797-1799.
4. Blais A, Dynlacht BD (2005) Constructing transcriptional regulatory networks. Genes Dev 19: 1499-1511.
5. Blais A, Tsikitis M, Acosta-Alvear D, Sharan R, Kluger Y, et al. (2005) An initial blueprint for myogenic differentiation. Genes Dev 19: 553-569.
6. Cao Y, Kumar RM, Penn BH, Berkes CA, Kooperberg C, et al. (2006) Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters. EMBO J 25: 502-511.
7. Farrall M (2004) Quantitative genetic variation: a post-modern view. Hum Mol Genet 13 Spec No 1: R1-7.
8. Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol 4: 162.
9. Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, et al. (2009) Learning a prior on regulatory potential from eQTL data. PLoS Genet 5: e1000358.
10. Hudson NJ, Reverter A, Dalrymple BP (2009) A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol 5: e1000382.
11. Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
12. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res 14: 1085-1094.
13. Carter SL, Brechbuhler CM, Griffin M, Bond AT (2004) Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 20: 2242-2250.
14. D'Haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16: 707-726.
15. Presson AP, Sobel EM, Papp JC, Suarez CJ, Whistler T, et al. (2008) Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. BMC Syst Biol 2: 95.
16. Zhang B, Horvath S (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4: Article17.
17. Reverter A, Hudson NJ, Wang Y, Tan SH, Barris W, et al. (2006) A gene coexpression network for bovine skeletal muscle inferred from microarray data. Physiol Genomics 28: 76-83.
18. Lehnert SA, Byrne KA, Reverter A, Nattrass GS, Greenwood PL, et al. (2006) Gene expression profiling of bovine skeletal muscle in response to and during recovery from chronic and severe undernutrition. J Anim Sci 84: 3239-3250.
19. Lehnert SA, Reverter A, Byrne KA, Wang Y, Nattrass GS, et al. (2007) Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds. BMC Dev Biol 7: 95.
20. Wang YH, Bower NI, Reverter A, Tan SH, De Jager N, et al. (2009) Gene expression patterns during intramuscular fat development in cattle. J Anim Sci 87: 119-130.
21. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10: 252-263.
22. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324: 1720-1723.
23. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, et al. (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133: 1266-1276.
24. Reverter A, Chan EK (2008) Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics 24: 2491-2497.
25. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.
26. Hudson NJ, Reverter A, Dalrymple BP (2009) A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Computational Biology (accepted).
27. Scherf M, Epple A, Werner T (2005) The next generation of literature analysis: integration of genomic analysis into text mining. Brief Bioinform 6: 287-297.
28. Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, et al. (2005) MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21: 2933-2942.
29. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
30. Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449.
31. Bottinelli R, Reggiani C (2000) Human skeletal muscle fibres: molecular and functional diversity. Prog Biophys Mol Biol 73: 195-262.
32. Sun X, Fontaine JM, Rest JS, Shelden EA, Welsh MJ, et al. (2004) Interaction of human HSP22 (HSPB8) with other small heat shock proteins. J Biol Chem 279: 2394-2402.
33. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10: 48.
34. Zampieri M, Soranzo N, Altafini C (2008) Discerning static and causal interactions in genome-wide reverse engineering problems. Bioinformatics 24: 1510-1515.
35. Villena JA, Hock MB, Chang WY, Barcas JE, Giguere V, et al. (2007) Orphan nuclear receptor estrogen-related receptor alpha is essential for adaptive thermogenesis. Proc Natl Acad Sci U S A 104: 1418-1423.
36. Matsui T, Kanai-Azuma M, Hara K, Matoba S, Hiramatsu R, et al. (2006) Redundant roles of Sox17 and Sox18 in postnatal angiogenesis in mice. J Cell Sci 119: 3513-3526.
37. Falkenberg M, Gaspari M, Rantanen A, Trifunovic A, Larsson NG, et al. (2002) Mitochondrial transcription factors B1 and B2 activate transcription of human mtDNA. Nat Genet 31: 289-294.
38. Qian Y, Fritzsch B, Shirasawa S, Chen CL, Choi Y, et al. (2001) Formation of brainstem (nor)adrenergic centers and first-order relay visceral sensory neurons is dependent on homeodomain protein Rnx/Tlx3. Genes Dev 15: 2533-2545.
39. Stolovitzky G, Prill RJ, Califano A (2009) Lessons from the DREAM2 Challenges. Ann N Y Acad Sci 1158: 159-195.
40. Watkinson J, Liang KC, Wang X, Zheng T, Anastassiou D (2009) Inference of regulatory gene interactions from expression data using three-way mutual information. Ann N Y Acad Sci 1158: 302-313.
41. Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, et al. (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37: 382-390.
42. Hartemink AJ (2005) Reverse engineering gene regulatory networks. Nat Biotechnol 23: 554-555.
43. Prieto C, Risueno A, Fontanillo C, De las Rivas J (2008) Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS ONE 3: e3911.
44. Brand MD, Couture P, Else PL, Withers KW, Hulbert AJ (1991) Evolution of energy metabolism. Proton permeability of the inner membrane of liver mitochondria is greater in a mammal than in a reptile. Biochem J 275(Pt 1): 81-86.
45. Hofmann WE, Liu X, Bearden CM, Harper ME, Kozak LP (2001) Effects of genetic background on thermoregulation and fatty acid-induced uncoupling of mitochondria in UCP1-deficient mice. J Biol Chem 276: 12460-12465.
46. Passos JF, von Zglinicki T (2005) Mitochondria, telomeres and cell senescence. Exp Gerontol 40: 466-472.
47. Hawley JA, Spargo FJ (2007) Metabolic adaptations to marathon training and racing. Sports Med 37: 328-331.
48. Finocchietto P, Barreyro F, Holod S, Peralta J, Franco MC, et al. (2008) Control of muscle mitochondria by insulin entails activation of Akt2-mtNOS pathway: implications for the metabolic syndrome. PLoS ONE 3: e1749.
49. Macintosh B, Gardiner P, McComas A (2006) Skeletal Muscle: Form and Function. .
50. Fuller TF, Ghazalpour A, Aten JE, Drake TA, Lusis AJ, et al. (2007) Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm Genome 18: 463-472.
51. Grifone R, Laclef C, Spitz F, Lopez S, Demignon J, et al. (2004) Six1 and Eya1 expression can reprogram adult muscle from the slow-twitch phenotype into the fast-twitch phenotype. Mol Cell Biol 24: 6253-6267.
52. Michoel T, De Smet R, Joshi A, Marchal K, Van de Peer Y (2009) Reverse-engineering transcriptional modules from gene expression data. Ann N Y Acad Sci 1158: 36-43.
53. Qin XQ, Barsoum J (1997) Differential cell cycle effects induced by E2F1 mutants. Oncogene 14: 53-62.
54. Gradin K, Takasaki C, Fujii-Kuriyama Y, Sogawa K (2002) The transcriptional activation function of the HIF-like factor requires phosphorylation at a conserved threonine. J Biol Chem 277: 23508-23514.
55. Liu B, Liao J, Rao X, Kushner SA, Chung CD, et al. (1998) Inhibition of Stat1-mediated gene activation by PIAS1. Proc Natl Acad Sci U S A 95: 10626-10631.
56. Rhee SD, Sung YY, Jung WH, Cheon HG (2008) Leptin inhibits rosiglitazone-induced adipogenesis in murine primary adipocytes. Mol Cell Endocrinol 294: 61-69.
57. Pine R (1992) Constitutive expression of an ISGF2/IRF1 transgene leads to interferon-independent activation of interferon-inducible genes and resistance to virus infection. J Virol 66: 4470-4478.
58. Issa LL, Palmer SJ, Guven KL, Santucci N, Hodgson VR, et al. (2006) MusTRD can regulate postnatal fiber-specific expression. Dev Biol 293: 104-115.
59. Lin J, Wu H, Tarr PT, Zhang CY, Wu Z, et al. (2002) Transcriptional coactivator PGC-1 alpha drives the formation of slow-twitch muscle fibres. Nature 418: 797-801.
60. Wang YX, Zhang CL, Yu RT, Cho HK, Nelson MC, et al. (2004) Regulation of muscle fiber type and running endurance by PPARdelta. PLoS Biol 2: e294.
61. McPherron AC, Lawler AM, Lee SJ (1997) Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member. Nature 387: 83-90.
62. Izumiya Y, Hopkins T, Morris C, Sato K, Zeng L, et al. (2008) Fast/ Glycolytic muscle fiber growth reduces fat mass and improves metabolic parameters in obese mice. Cell Metab 7: 159-172.
63. Berry C, Thomas M, Langley B, Sharma M, Kambadur R (2002) Single cysteine to tyrosine transition inactivates the growth inhibitory function of Piedmontese myostatin. Am J Physiol Cell Physiol 283: C135-141.
64. Almenar-Queralt A, Lee A, Conley CA, Ribas de Pouplana L, Fowler VM (1999) Identification of a novel tropomodulin isoform, skeletal tropomodulin, that caps actin filament pointed ends in fast skeletal muscle. J Biol Chem 274: 28466-28475.
65. Bicer S, Reiser PJ (2004) Myosin light chain isoform expression among single mammalian skeletal muscle fibers: species variations. J Muscle Res Cell Motil 25: 623-633.
66. Petrovic V, Costa RH, Lau LF, Raychaudhuri P, Tyner AL (2008) FoxM1 regulates growth factor-induced expression of kinase-interacting stathmin (KIS) to promote cell cycle progression. J Biol Chem 283: 453-460.
67. Christensen J, Cloos P, Toftegaard U, Klinkenberg D, Bracken AP, et al. (2005) Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription. Nucleic Acids Res 33: 5458-5470.
68. Johnson DG, Ohtani K, Nevins JR (1994) Autoregulatory control of E2F1 expression in response to positive and negative regulators of cell cycle progression. Genes Dev 8: 1514-1525.
69. Chen Q, Hung FC, Fromm L, Overbeek PA (2000) Induction of cell cycle entry and cell death in postmitotic lens fiber cells by overexpression of E2F1 or E2F2. Invest Ophthalmol Vis Sci 41: 4223-4231.
70. De La Fuente R, Baumann C, Fan T, Schmidtmann A, Dobrinski I, et al. (2006) Lsh is required for meiotic chromosome synapsis and retrotransposon silencing in female germ cells. Nat Cell Biol 8: 1448-1454.
71. McCleland ML, Gardner RD, Kallio MJ, Daum JR, Gorbsky GJ, et al. (2003) The highly conserved Ndc80 complex is required for kinetochore assembly, chromosome congression, and spindle checkpoint activity. Genes Dev 17: 101-114.
72. Watt PM, Hickson ID (1994) Structure and function of type II DNA topoisomerases. Biochem J 303(Pt 3): 681-695.
73. Hayashi R, Goto Y, Ikeda R, Yokoyama KK, Yoshida K (2006) CDCA4 is an E2F transcription factor family-induced nuclear factor that regulates E2F-dependent transcriptional activation and cell proliferation. J Biol Chem 281: 35633-35648.
74. Liu L, Xu AG, Zhang QL, Zhang YF, Ding YQ (2007) [Effect of Tiam1 overexpression on proliferation and metastatic potential of human colorectal cancer]. Zhonghua Bing Li Xue Za Zhi 36: 390-393.
75. Hong SK, Han SB, Snyder M, Choi EY (1999) SHC1, a high pH inducible gene required for growth at alkaline pH in Saccharomyces cerevisiae. Biochem Biophys Res Commun 255: 116-122.
76. Chiu CH, Lin WD, Huang SY, Lee YH (2004) Effect of a C/EBP gene replacement on mitochondrial biogenesis in fat cells. Genes Dev 18: 1970-1975.
77. Setoyama C (1995) [Molecular mechanisms of the expression of cytosolic and mitochondrial isozyme genes]. Nippon Rinsho 53: 1081-1086.
78. Xu Y, Liu YJ, Yu Q (2004) Angiopoietin-3 is tethered on the cell surface via heparan sulfate proteoglycans. J Biol Chem 279: 41179-41188.
79. Sage EH, Bornstein P (1991) Extracellular proteins that modulate cell-matrix interactions. SPARC, tenascin, and thrombospondin. J Biol Chem 266: 14831-14834.
80. Ong VH, Carulli MT, Xu S, Khan K, Lindahl G, et al. (2009) Cross-talk between MCP-3 and TGFbeta promotes fibroblast collagen biosynthesis. Exp Cell Res 315: 151-161.
81. Sander EE, van Delft S, ten Klooster JP, Reid T, van der Kammen RA, et al. (1998)Matrix-dependent Tiam1/Rac signaling in epithelial cells promotes either cell-cell adhesion or cell migration and is regulated by phosphatidylinositol 3-kinase. J Cell Biol 143: 1385-1398.
82. Cohen DR, Cheng CW, Cheng SH, Hui CC (2000) Expression of two novel mouse Iroquois homeobox genes during neurogenesis. Mech Dev 91: 317-321.
83. Barnes JD, Crosby JL, Jones CM, Wright CV, Hogan BL (1994) Embryonic expression of Lim-1, the mouse homolog of Xenopus Xlim-1, suggests a role in lateral mesoderm differentiation and neurogenesis. Dev Biol 161: 168-178.
84. de la Cruz CC, Der-Avakian A, Spyropoulos DD, Tieu DD, Carpenter EM (1999) Targeted disruption of Hoxd9 and Hoxd10 alters locomotor behavior, vertebral identity, and peripheral nervous system development. Dev Biol 216: 595-610.
85. Sheng HZ, Bertuzzi S, Chiang C, Shawlot W, Taira M, et al. (1997) Expression of murine Lhx5 suggests a role in specifying the forebrain. Dev Dyn 208: 266-277.
86. Akazawa C, Sasai Y, Nakanishi S, Kageyama R (1992) Molecular characterization of a rat negative regulator with a basic helix-loop-helix structure predominantly expressed in the developing nervous system. J Biol Chem 267: 21879-21885.
87. Leid M, Ishmael JE, Avram D, Shepherd D, Fraulob V, et al. (2004) CTIP1 and CTIP2 are differentially expressed during mouse embryogenesis. Gene Expr Patterns 4: 733-739.
88. Toresson H, Mata de Urquiza A, Fagerstrom C, Perlmann T, Campbell K (1999) Retinoids are produced by glia in the lateral ganglionic eminence and regulate striatal neuron differentiation. Development 126: 1317-1326.
89. Holland PW, Holland LZ, Williams NA, Holland ND (1992) An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution. Development 116: 653-661.
90. Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, et al. (2002) Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development. Proc Natl Acad Sci U S A 99: 14320-14325.