An Always Correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an "equivalent" bovine landscape

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Sun, Wei ^a,b   Hudson, Nicholas J ^b   Reverter, Antonio ^b   Waardenberg, Ashley J ^b   Tellam, Ross L ^b   Vuocolo, Tony ^b   Byrne, Keren ^b   Dalrymple, Brian P ^b  

^a YANGZHOU UNIVERSITY   (China)

^b CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BOS; BOVINAE; OVIS; OVIS ARIES;

MUSCLE PROTEIN;

ANIMAL; ARTICLE; BIOLOGY; CATTLE; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; MUSCLE DEVELOPMENT; PHENOTYPE; REPRODUCIBILITY; SHEEP; SKELETAL MUSCLE; SPECIES DIFFERENCE;

ANIMALS; CATTLE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENOTYPE; MUSCLE DEVELOPMENT; MUSCLE PROTEINS; MUSCLE, SKELETAL; PHENOTYPE; REPRODUCIBILITY OF RESULTS; SHEEP; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC;

MLCS; MLOWN;

EID: 84868655299     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-632     Document Type: Article

References (32)

1. Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks. Hudson NJ, Reverter A, Wang Y, Greenwood PL, Dalrymple BP, PLoS One 2009 4 10 7249 10.1371/journal.pone.0007249 19794913
2. Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle. Mariasegaram M, Reverter A, Barris W, Lehnert SA, Dalrymple B, Prayaga K, BMC Genomics 2010 11 1 370 10.1186/1471-2164-11-370 20537189
3. Robust estimators for expression analysis. Hubbell E, Liu WM, Mei R, Bioinformatics 2002 18 12 1585 1592 10.1093/bioinformatics/18.12.1585 12490442 (Pubitemid 36097723)
4. A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development. Byrne K, Vuocolo T, Gondro C, White JD, Cockett NE, Hadfield T, Bidwell CA, Waddell JN, Tellam RL, BMC Genomics 2010 11 378 10.1186/1471-2164-11-378 20546621
5. Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle. Vuocolo T, Byrne K, White J, McWilliam S, Reverter A, Cockett NE, Tellam RL, Physiol Genomics 2007 28 3 253 272 17077277 (Pubitemid 46711003)
6. Analysis of gene expression during the onset of muscle hypertrophy in callipyge lambs. Fleming-Waddell JN, Wilson LM, Olbricht GR, Vuocolo T, Byrne K, Craig BA, Tellam RL, Cockett NE, Bidwell CA, Anim Genet 2007 38 1 28 36 10.1111/j.1365-2052.2006.01562.x 17257185 (Pubitemid 46174900)
7. Genetic architecture of gene expression in ovine skeletal muscle. Kogelman LJ, Byrne K, Vuocolo T, Watson-Haigh NS, Kadarmideen HN, Kijas JW, Oddy HV, Gardner GE, Gondro C, Tellam RL, BMC Genomics 2011 12 607 10.1186/1471-2164-12-607 22171619
8. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Reverter A, Chan EK, Bioinformatics 2008 24 21 2491 2497 10.1093/bioinformatics/btn482 18784117
9. PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. Watson-Haigh NS, Kadarmideen HN, Reverter A, Bioinformatics 2010 26 3 411 413 10.1093/bioinformatics/btp674 20007253
10. An automated method for finding molecular complexes in large protein interaction networks. Bader GD, Hogue CW, BMC Bioinformatics 2003 4 2 10.1186/1471-2105-4-2 12525261 (Pubitemid 38751268)
11. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Maere S, Heymans K, Kuiper M, Bioinformatics 2005 21 16 3448 3449 10.1093/bioinformatics/bti551 15972284 (Pubitemid 41222459)
12. Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle. Waardenberg AJ, Reverter A, Wells CA, Dalrymple BP, BMC Syst Biol 2008 2 88 10.1186/1752-0509-2-88 18945372
13. Human skeletal muscle fibres: molecular and functional diversity. Bottinelli R, Reggiani C, Prog Biophys Mol Biol 2000 73 2-4 195 262 10958931
14. Identification of a novel tropomodulin isoform, skeletal tropomodulin, that caps actin filament pointed ends in fast skeletal muscle. Almenar-Queralt A, Lee A, Conley CA, Ribas De Pouplana L, Fowler VM, J Biol Chem 1999 274 40 28466 28475 10.1074/jbc.274.40.28466 10497209 (Pubitemid 29472972)
15. Myosin light chain isoform expression among single mammalian skeletal muscle fibers: species variations. Bicer S, Reiser PJ, J Muscle Res Cell Motil 2004 25 8 623 633 10.1007/s10974-004-5070-9 15750847 (Pubitemid 40562028)
16. Identification and characterization of human Fas associated factor 1, hFAF1. Ryu SW, Chae SK, Lee KJ, Kim E, Biochem Biophys Res Commun 1999 262 2 388 394 10.1006/bbrc.1999.1217 10462485 (Pubitemid 29429878)
17. Isolation of mammalian 26S proteasomes and p97/VCP complexes using the ubiquitin-like domain from HHR23B reveals novel proteasome-associated proteins. Besche HC, Haas W, Gygi SP, Goldberg AL, Biochemistry 2009 48 11 2538 2549 10.1021/bi802198q 19182904
18. UBX domain proteins: major regulators of the AAA ATPase Cdc48/p97. Schuberth C, Buchberger A, Cell Mol Life Sci 2008 65 15 2360 2371 10.1007/s00018-008-8072-8 18438607
19. Valosin-containing protein disease: inclusion body myopathy with Paget's disease of the bone and fronto-temporal dementia. Weihl CC, Pestronk A, Kimonis VE, Neuromuscul Disord 2009 19 5 308 315 10.1016/j.nmd.2009.01.009 19380227
20. The ubiquitin-proteasome pathway: review of a novel intracellular mechanism of muscle protein breakdown during sepsis and other catabolic conditions. Hasselgren PO, Fischer JE, Ann Surg 1997 225 3 307 316 10.1097/00000658-199703000-00011 9060588 (Pubitemid 27131568)
21. A muscle hypertrophy condition in lamb (callipyge): characterization of effects on muscle growth and meat quality traits. Koohmaraie M, Shackelford SD, Wheeler TL, Lonergan SM, Doumit ME, J Anim Sci 1995 73 12 3596 3607 8655433
22. Genetic and environmental effects on meat quality. Warner RD, Greenwood PL, Pethick DW, Ferguson DM, Meat Sci 2010 86 1 171 183 10.1016/j.meatsci.2010. 04.042 20561754
23. A hypoplastic model of skeletal muscle development displaying reduced foetal myoblast cell numbers, increased oxidative myofibres and improved specific tension capacity. Otto A, Macharia R, Matsakas A, Valasek P, Mankoo BS, Patel K, Dev Biol 2010 343 1-2 51 62 20417199
24. Mammalian COP9 signalosome. Kato JY, Yoneda-Kato N, Genes Cells 2009 14 11 1209 1225 10.1111/j.1365-2443.2009.01349.x 19849719
25. JAB1 accelerates mitochondrial apoptosis by interaction with proapoptotic BclGs. Liu X, Pan Z, Zhang L, Sun Q, Wan J, Tian C, Xing G, Yang J, Jiang J, He F, Cell Signal 2008 20 1 230 240 10.1016/j.cellsig.2007.10.012 18006276 (Pubitemid 350138384)
26. Novel DNA mismatch-repair activity involving YB-1 in human mitochondria. de Souza-Pinto NC, Mason PA, Hashiguchi K, Weissman L, Tian J, Guay D, Lebel M, Stevnsner TV, Rasmussen LJ, Bohr VA, DNA Repair (Amst) 2009 8 6 704 719 10.1016/j.dnarep.2009.01.021
27. Signalling cross talk of the HIF system: involvement of the FIH protein. Coleman ML, Ratcliffe PJ, Curr Pharm Des 2009 15 33 3904 3907 10.2174/138161209789649448 19671041
28. Inter-connection between mitochondria and HIFs. Tormos KV, Chandel NS, J Cell Mol Med 2010 14 4 795 804 10.1111/j.1582-4934.2010.01031.x 20158574
29. The architecture of mammalian ribosomal protein promoters. Perry RP, BMC Evol Biol 2005 5 1 15 10.1186/1471-2148-5-15 15707503 (Pubitemid 40553347)
30. COP9-associated CSN5 regulates exosomal protein deubiquitination and sorting. Liu Y, Shah SV, Xiang X, Wang J, Deng ZB, Liu C, Zhang L, Wu J, Edmonds T, Jambor C, et al. Am J Pathol 2009 174 4 1415 1425 10.2353/ajpath.2009.080861 19246649
31. Ubc9 interacts with SOX4 and represses its transcriptional activity. Pan X, Li H, Zhang P, Jin B, Man J, Tian L, Su G, Zhao J, Li W, Liu H, et al. Biochem Biophys Res Commun 2006 344 3 727 734 10.1016/j.bbrc.2006.03.194 16631117
32. Positive reciprocal regulation of ubiquitin C-terminal hydrolase L1 and beta-catenin/TCF signaling. Bheda A, Yue W, Gullapalli A, Whitehurst C, Liu R, Pagano JS, Shackelford J, PLoS One 2009 4 6 5955 10.1371/journal.pone.0005955 19536331