{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T02:02:54Z","timestamp":1789956174017,"version":"4.0.1"},"reference-count":67,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2015,6,4]],"date-time":"2015-06-04T00:00:00Z","timestamp":1433376000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0128350","type":"journal-article","created":{"date-parts":[[2015,6,4]],"date-time":"2015-06-04T18:49:38Z","timestamp":1433443778000},"page":"e0128350","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":90,"title":["Putative Regulatory Factors Associated with Intramuscular Fat Content"],"prefix":"10.1371","volume":"10","author":[{"given":"Aline S. M.","family":"Cesar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciana C. A.","family":"Regitano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Koltes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric R.","family":"Fritz-Waters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dante P. D.","family":"Lanna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustavo","family":"Gasparin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerson B.","family":"Mour\u00e3o","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priscila S. N.","family":"Oliveira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M.","family":"Reecy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz L.","family":"Coutinho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2015,6,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1111\/j.1365-2052.2006.01464.x","article-title":"The bovine fatty acid binding protein 4 gene is significantly associated with marbling and subcutaneous fat depth in Wagyu x Limousin F2 crosses","volume":"37","author":"JJ Michal","year":"2006","journal-title":"Anim Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1525","DOI":"10.2527\/1997.7561525x","article-title":"Influence of sire growth potential, time on feed, and growing-finishing strategy on cholesterol and fatty acids of the ground carcass and longissimus muscle of beef steers","volume":"75","author":"DC Rule","year":"1997","journal-title":"J Anim Sci"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"626","DOI":"10.2527\/jas.2011-4282","article-title":"Consumer assessment of beef strip loin steaks of varying fat levels","volume":"90","author":"TG O'Quinn","year":"2012","journal-title":"J Anim Sci"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"20","DOI":"10.2527\/af.2013-0004","article-title":"Impact of consumption of animal products on cardiovascular disease, diabetes, and cancer in developed countries","volume":"3","author":"AM Salter","year":"2013","journal-title":"Anim Front"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1016\/j.meatsci.2013.07.031","article-title":"Modelling of beef sensory quality for a better prediction of palatability","volume":"97","author":"JF Hocquette","year":"2013","journal-title":"Meat Sci"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1186\/1471-2164-13-547","article-title":"Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition","volume":"13","author":"Y Ramayo-Caldas","year":"2012","journal-title":"BMC Genomics"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"171","DOI":"10.2527\/jas.2011-4229","article-title":"Transcriptome analysis of subcutaneous adipose tissues in beef cattle using 3&apos; digital gene expression-tag profiling","volume":"90","author":"W Jin","year":"2012","journal-title":"J Anim Sci"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.2527\/jas.2012-5409","article-title":"Gene expression phenotypes for lipid metabolism and intramuscular fat in skeletal muscle of cattle","volume":"91","author":"N De Jager","year":"2013","journal-title":"J Anim Sci"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.2527\/jas.2013-7484","article-title":"A marker-derived gene network reveals the regulatory role of PPARGC1A, HNF4G, and FOXP3 in intramuscular fat deposition of beef cattle","volume":"92","author":"Y Ramayo-Caldas","year":"2014","journal-title":"J Anim Sci"},{"key":"ref10","first-page":"1","article-title":"In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","author":"L Koesterke","year":"2013"},{"key":"ref11","first-page":"e1000382","article-title":"A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation","volume":"5","author":"NJ Hudson","year":"2009"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1471-2156-15-39","article-title":"Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle","volume":"15","author":"AS Cesar","year":"2014","journal-title":"BMC Genet"},{"key":"ref13","article-title":"Official Procedure Am 5\u201304 oil. Official Methods and Recommended Practices of the AOCS.","year":"2004"},{"key":"ref14","article-title":"ASReml User Guide Release 3.0 Hemel Hempstead, HP1 1ES","author":"AR Gilmour","year":"2009"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"4414","DOI":"10.3168\/jds.2007-0980","article-title":"Efficient methods to compute genomic predictions","volume":"91","author":"PM VanRaden","year":"2008","journal-title":"J Dairy Sci"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"S Anders","year":"2009","journal-title":"Genome Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J Roy Statist Soc Ser B"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1093\/nar\/gkq1115","article-title":"AgBase: supporting functional modeling in agricultural organisms","volume":"39","author":"FM McCarthy","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"W Huang da","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1093\/bioinformatics\/btg290","article-title":"Pathway studio\u2014the analysis and navigation of molecular networks","volume":"19","author":"A Nikitin","year":"2003","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.1093\/bioinformatics\/btn482","article-title":"Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks","volume":"24","author":"A Reverter","year":"2008","journal-title":"Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1093\/bioinformatics\/btq051","article-title":"Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data","volume":"26","author":"A Reverter","year":"2010","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.meatsci.2010.04.034","article-title":"The support of meat value chains by genetic technologies","volume":"86","author":"AA Sosnicki","year":"2010","journal-title":"Meat Sci"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1146\/annurev-immunol-031210-101322","article-title":"Inflammatory mechanisms in obesity","volume":"29","author":"MF Gregor","year":"2011","journal-title":"Annu Rev Immunol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1152\/physrev.1998.78.3.783","article-title":"Understanding adipocyte differentiation","volume":"78","author":"FM Gregoire","year":"1998","journal-title":"Physiol Rev"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrm3198","article-title":"Forming functional fat: a growing understanding of adipocyte differentiation","volume":"12","author":"AG Cristancho","year":"2011","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref29","first-page":"757","article-title":"Identification of differentially expressed genes related to intramuscular fat development in the early and late fattening stages of hanwoo steers","volume":"40","author":"SH Lee","year":"2007","journal-title":"J Biochem Mol Biol"},{"issue":"6","key":"ref30","doi-asserted-by":"crossref","first-page":"e66267","DOI":"10.1371\/journal.pone.0066267","article-title":"Comparative Transcriptome Analysis of Adipose Tissues Reveals that ECM-Receptor Interaction Is Involved in the Depot-Specific Adipogenesis in Cattle","volume":"8","author":"HJ Lee","year":"2013","journal-title":"PLoS One"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/s00335-004-2419-8","article-title":"Transcriptional profiling of skeletal muscle tissue from two breeds of cattle","volume":"16","author":"YH Wang","year":"2005","journal-title":"Mamm Genome"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"6045","DOI":"10.1073\/pnas.1030790100","article-title":"SPARC-null mice exhibit increased adiposity without significant differences in overall body weight","volume":"100","author":"AD Bradshaw","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/s12079-009-0064-4","article-title":"SPARC functions as an inhibitor of adipogenesis","volume":"3","author":"J Nie","year":"2009","journal-title":"J Cell Commun Signal"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1038\/emboj.2011.80","article-title":"Adipogenic hotspots: where the action is","volume":"30","author":"DJ Steger","year":"2011","journal-title":"EMBO J"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"12","DOI":"10.4161\/nucl.18928","article-title":"Modulation of chromatin access during adipocyte differentiation","volume":"3","author":"S Mandrup","year":"2012","journal-title":"Nucleus"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0960-0760(99)00052-7","article-title":"Interactions in the transcriptional regulation exerted by Stat5 and by members of the steroid hormone receptor family","volume":"69","author":"E Stoecklin","year":"1999","journal-title":"J Steroid Biochem Mol Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1101\/gr.2596504","article-title":"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)","volume":"14","author":"DS Gerhard","year":"2004","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"756","DOI":"10.2527\/jas.2009-1951","article-title":"Intramuscular fat and fatty acid composition of longissimus muscle from divergent pure breeds of cattle","volume":"88","author":"TT Dinh","year":"2010","journal-title":"J Anim Sci"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/1471-213X-7-95","article-title":"Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds","volume":"7","author":"SA Lehnert","year":"2007","journal-title":"BMC Dev Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"119","DOI":"10.2527\/jas.2008-1082","article-title":"Gene expression patterns during intramuscular fat development in cattle","volume":"87","author":"YH Wang","year":"2009","journal-title":"J Anim Sci"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"49","DOI":"10.4141\/A02-058","article-title":"Expression of peroxisome proliterator-activated receptor (PPAR\u03b3) mRNA in adipose and muscle tissue of Holstein and Charolais cattle","volume":"84","author":"PW Huff","year":"2004","journal-title":"Can J Anim Sci"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/S0968-0004(00)89004-0","article-title":"The dynamic role of palmitoylation in signal transduction","volume":"20","author":"G Milligan","year":"1995","journal-title":"Trends Biochem Sci"},{"key":"ref43","first-page":"re14","article-title":"Palmitoylation of ligands, receptors, and intracellular signaling molecules","volume":"359","author":"MD Resh","year":"2006","journal-title":"Sci STKE"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"461","DOI":"10.2310\/6650.2006.06009","article-title":"Abnormal levels of serum antielastin antibodies in children with diabetes mellitus type 1","volume":"54","author":"G Nicoloff","year":"2006","journal-title":"J Investig Med"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.nbd.2011.06.012","article-title":"Obesity and downregulated hypothalamic leptin receptors in male metallothionein-3-null mice","volume":"44","author":"HR Byun","year":"2011","journal-title":"Neurobiol Dis"},{"key":"ref46","first-page":"457","article-title":"Insulin resistance does not influence gene expression in skeletal muscle","volume":"39","author":"LL Nguyen","year":"2006","journal-title":"J Biochem Mol Biol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1038\/35055575","article-title":"Adipose-selective targeting of the GLUT4 gene impairs insulin action in muscle and liver","volume":"409","author":"ED Abel","year":"2001","journal-title":"Nature"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"684159","DOI":"10.1155\/2013\/684159","article-title":"Functional Role of PPARs in Ruminants: Potential Targets for Fine-Tuning Metabolism during Growth and Lactation","volume":"2013","author":"M Bionaz","year":"2013","journal-title":"PPAR Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1007\/s00125-011-2263-9","article-title":"Partial inactivation of Ankrd26 causes diabetes with enhanced insulin responsiveness of adipose tissue in mice","volume":"54","author":"GA Raciti","year":"2011","journal-title":"Diabetologia"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"14","DOI":"10.7150\/jca.1.14","article-title":"Tumor Suppressor RARRES1 Regulates DLG2, PP2A, VCP, EB1, and Ankrd26","volume":"1","author":"ZJ Sahab","year":"2010","journal-title":"J Cancer"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1002\/j.1460-2075.1992.tb05049.x","article-title":"The upstream region of the human homeobox gene HOX3D is a target for regulation by retinoic acid and HOX homeoproteins","volume":"11","author":"L Arcioni","year":"1992","journal-title":"EMBO J"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1006\/bbrc.1997.7160","article-title":"Developmental profile of homeobox gene expression during 3T3-L1 adipogenesis","volume":"237","author":"RM Cowherd","year":"1997","journal-title":"Biochem Biophys Res Commun"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.plipres.2006.01.005","article-title":"Signaling functions of phosphatidic acid","volume":"45","author":"X Wang","year":"2006","journal-title":"Prog Lipid Res"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1126\/science.1096083","article-title":"Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid","volume":"304","author":"CJ Loewen","year":"2004","journal-title":"Science"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"12355","DOI":"10.1073\/pnas.93.22.12355","article-title":"Arrested development of embryonic red cell precursors in mouse embryos lacking transcription factor GATA-1","volume":"93","author":"Y Fujiwara","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"4101","DOI":"10.1007\/s11033-011-1192-5","article-title":"Variation in the IGF2 gene promoter region is associated with intramuscular fat content in porcine skeletal muscle","volume":"39","author":"O Aslan","year":"2012","journal-title":"Mol Biol Rep"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1101\/gr.074914.107","article-title":"A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility","volume":"18","author":"MP Keller","year":"2008","journal-title":"Genome Res"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/nrc3174","article-title":"Molecular mechanisms of cancer development in obesity","volume":"11","author":"MJ Khandekar","year":"2011","journal-title":"Nature Reviews Cancer"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1242\/dev.016204","article-title":"Early mouse caudal development relies on crosstalk between retinoic acid, Shh and Fgf signalling pathways","volume":"136","author":"V Ribes","year":"2009","journal-title":"Development"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/clpt.2013.10","article-title":"Clinical proof-of-concept study with MSDC-0160, a prototype mTOT-modulating insulin sensitizer","volume":"93","author":"JR Colca","year":"2013","journal-title":"Clin Pharmacol Ther"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1111\/j.1365-2052.2011.02252.x","article-title":"Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace x Chinese-European crossbred population","volume":"43","author":"S Cepica","year":"2012","journal-title":"Anim Genet"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1353\/hub.2006.0033","article-title":"Association of genetic variation within UBL5 with phenotypes of metabolic syndrome","volume":"78","author":"K Bozaoglu","year":"2006","journal-title":"Hum Biol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"2467","DOI":"10.2337\/diabetes.53.9.2467","article-title":"Genetic variation in BEACON influences quantitative variation in metabolic syndrome-related phenotypes","volume":"53","author":"JB Jowett","year":"2004","journal-title":"Diabetes"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1038\/cdd.2013.181","article-title":"Suppression of PPAR\u03b3 through MKRN1-mediated ubiquitination and degradation prevents adipocyte differentiation","volume":"21","author":"JH Kim","year":"2014","journal-title":"Cell Death Differ"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1186\/1471-2164-15-137","article-title":"MicroRNAs in bovine adipogenesis: genomic context, expression and function","volume":"15","author":"JM Romao","year":"2014","journal-title":"BMC Genomics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.2527\/jas.2008-1427","article-title":"Board-invited review: The biology and regulation of preadipocytes and adipocytes in meat animals","volume":"87","author":"GJ Hausman","year":"2009","journal-title":"J Anim Sci"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/S0248-4900(02)01189-9","article-title":"Extracellular matrix development during differentiation into adipocytes with a unique increase in type V and VI collagen","volume":"94","author":"I Nakajima","year":"2002","journal-title":"Biol Cell"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0128350","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,9]],"date-time":"2024-06-09T10:33:27Z","timestamp":1717929207000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0128350"}},"subtitle":[],"editor":[{"given":"Roberta","family":"Davoli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2015,6,4]]},"references-count":67,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2015,6,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0128350","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,6,4]]}}}