{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T12:08:18Z","timestamp":1767182898284,"version":"build-2238731810"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2018,9,21]],"date-time":"2018-09-21T00:00:00Z","timestamp":1537488000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["R01 HL081690"],"award-info":[{"award-number":["R01 HL081690"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0204100","type":"journal-article","created":{"date-parts":[[2018,9,21]],"date-time":"2018-09-21T14:08:09Z","timestamp":1537538889000},"page":"e0204100","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Biologically anchored knowledge expansion approach uncovers KLF4 as a novel insulin signaling regulator"],"prefix":"10.1371","volume":"13","author":[{"given":"Annamalai","family":"Muthiah","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Morgan S.","family":"Angulo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0223-0611","authenticated-orcid":true,"given":"Natalie N.","family":"Walker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3089-7766","authenticated-orcid":true,"given":"Susanna R.","family":"Keller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2343-5205","authenticated-orcid":true,"given":"Jae K.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,9,21]]},"reference":[{"issue":"4","key":"ref1","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/ng1532","article-title":"Reverse engineering of regulatory net-works in human B cells","volume":"37","author":"K Basso","year":"2005","journal-title":"Nat Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"D866","DOI":"10.1093\/nar\/gkr1050","article-title":"Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks","volume":"40","author":"B Haibe-Kains","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ref3","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/ng1165","article-title":"Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data","volume":"34","author":"E Segal","year":"2003","journal-title":"Nat Genet"},{"issue":"12","key":"ref4","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"PT Spellman","year":"1998","journal-title":"Mol Biol Cell"},{"issue":"1","key":"ref5","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","article-title":"Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles","volume":"5","author":"JJ Faith","year":"2007","journal-title":"PLoS Biol"},{"issue":"48","key":"ref6","doi-asserted-by":"crossref","first-page":"19436","DOI":"10.1073\/pnas.1116442108","article-title":"Construction of regulatory networks using expres-sion time-series data of a genotyped population","volume":"108","author":"KY Yeung","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6062","key":"ref7","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1126\/science.1205438","article-title":"Detecting novel associations in large data sets","volume":"334","author":"DN Reshef","year":"2011","journal-title":"Science"},{"issue":"91","key":"ref8","doi-asserted-by":"crossref","first-page":"20130505","DOI":"10.1098\/rsif.2013.0505","article-title":"Reverse engineering and identification in systems biology: strategies, perspectives and chal-lenges","volume":"11","author":"AF Villaverde","year":"2013","journal-title":"J R Soc Interface"},{"issue":"Suppl 1","key":"ref9","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2105-7-S1-S7","article-title":"ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context","volume":"7","author":"AA Margolin","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/1471-2105-11-154","article-title":"TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach","volume":"11","author":"P Zoppoli","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1186\/1471-2105-9-467","article-title":"Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information","volume":"9","author":"W Luo","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref12","first-page":"418","article-title":"Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements","author":"AJ Butte","year":"2000","journal-title":"Pac Symp Biocomput"},{"key":"ref13","first-page":"79879","article-title":"Information-theoretic inference of large transcriptional regulatory net-works","author":"PE Meyer","year":"2007","journal-title":"EURASIP J Bioinform Syst Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/1752-0509-4-132","article-title":"Inferring the conservative causal core of gene regulatory networks","volume":"4","author":"G Altay","year":"2010","journal-title":"BMC Syst Biol"},{"issue":"18","key":"ref15","doi-asserted-by":"crossref","first-page":"3565","DOI":"10.1093\/bioinformatics\/bth445","article-title":"Discovery of meaningful associations in genomic data using partial correlation coefficients","volume":"20","author":"A de la Fuente","year":"2004","journal-title":"Bioinformatics"},{"issue":"4","key":"ref16","first-page":"730","article-title":"Genome-wide partial correlation analysis of Esche-richia coli microarray data","volume":"6","author":"DF Veiga","year":"2007","journal-title":"Genet Mol Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1007\/978-1-61779-400-1_13","article-title":"Nonhomogeneous dynamic Bayesian networks in systems biology","volume":"802","author":"S Lebre","year":"2012","journal-title":"Methods Mol Biol"},{"issue":"1","key":"ref18","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1093\/bioinformatics\/btp619","article-title":"Simulation-based model selection for dynamical systems in systems and population biology","volume":"26","author":"T Toni","year":"2010","journal-title":"Bioinformatics"},{"issue":"9","key":"ref19","doi-asserted-by":"crossref","first-page":"e12776","DOI":"10.1371\/journal.pone.0012776","article-title":"Inferring regulatory networks from expression data using tree-based methods","volume":"5","author":"VA Huynh-Thu","year":"2010","journal-title":"PLoS One"},{"issue":"4","key":"ref20","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/bioinformatics\/bti816","article-title":"Least absolute regression network analysis of the murine osteoblast differentiation network","volume":"22","author":"EP van Someren","year":"2006","journal-title":"Bioinformatics"},{"issue":"26","key":"ref21","doi-asserted-by":"crossref","first-page":"15522","DOI":"10.1073\/pnas.2136632100","article-title":"Network component analysis: reconstruction of regulatory signals in biological systems","volume":"100","author":"JC Liao","year":"2003","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"ref22","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/nmeth.2016","article-title":"Wisdom of crowds for robust gene net-work inference","volume":"9","author":"D Marbach","year":"2012","journal-title":"Nat Methods"},{"issue":"11","key":"ref23","doi-asserted-by":"crossref","first-page":"e1003361","DOI":"10.1371\/journal.pcbi.1003361","article-title":"Harnessing Diversity towards the Reconstructing of Large Scale Gene Re-gulatory Networks","volume":"9","author":"T Hase","year":"2013","journal-title":"PLoS Comput Biol"},{"issue":"5","key":"ref24","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng0506-500","article-title":"GenePattern 2.0","volume":"38","author":"M Reich","year":"2006","journal-title":"Nat Genet"},{"issue":"8","key":"ref25","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/ng.2355","article-title":"Leveraging models of cell regulation and GWAS data in integra-tive network-based association studies","volume":"44","author":"A Califano","year":"2012","journal-title":"Nat Genet"},{"issue":"3","key":"ref26","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s00109-006-0138-1","article-title":"Dietary fat, genes and insulin sensitivity","volume":"85","author":"J Lopez-Miranda","year":"2007","journal-title":"J Mol Med (Berl)"},{"issue":"4","key":"ref27","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1016\/S0092-8674(00)81896-6","article-title":"Development of a novel polygenic model of NIDDM in mice heterozygous for IR and IRS-1 null alleles","volume":"88","author":"JC Bruning","year":"1997","journal-title":"Cell"},{"issue":"2","key":"ref28","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1161\/ATVBAHA.111.240358","article-title":"Accelerated atherosclerosis in Apoe-\/- mice hetero-zygous for the insulin receptor and the insulin receptor substrate-1","volume":"32","author":"EV Galkina","year":"2012","journal-title":"Arterioscler Thromb Vasc Biol"},{"issue":"10","key":"ref29","doi-asserted-by":"crossref","first-page":"E1273","DOI":"10.1152\/ajpendo.00316.2012","article-title":"Deletion of Rab GAP AS160 modifies glucose uptake and GLUT4 translocation in primary skeletal muscles and adipocytes and impairs glucose homeostasis","volume":"303","author":"MN Lansey","year":"2012","journal-title":"Am J Physiol Endocrinol Metab"},{"key":"ref30","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1027","article-title":"Linear models and empirical bayes methods for assessing differential expression in microarray experi-ments","volume":"3","author":"GK Smyth","year":"2004","journal-title":"Stat Appl Genet Mol Biol"},{"issue":"9","key":"ref31","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"VG Tusher","year":"2001","journal-title":"Proc Natl Acad Sci USA"},{"issue":"18","key":"ref32","doi-asserted-by":"crossref","first-page":"3251","DOI":"10.1103\/PhysRevLett.76.3251","article-title":"Superparamagnetic clustering of data","volume":"76","author":"M Blatt","year":"1996","journal-title":"Phys Rev Lett"},{"issue":"12","key":"ref33","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1161\/CIRCRESAHA.108.176974","article-title":"Conditional deletion of Kruppel-like factor 4 delays downregulation of smooth muscle cell differentiation markers but accelerates neointimal formation following vascular injury","volume":"102","author":"T Yoshida","year":"2008","journal-title":"Circ Res"},{"issue":"10","key":"ref34","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1002\/oby.20811","article-title":"Variations in body weight, food intake and body composi-tion after long-term high-fat diet feeding in C57BL\/6J mice","volume":"22","author":"Y Yang","year":"2014","journal-title":"Obesity (Silver Spring)"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"E207","DOI":"10.1152\/ajpendo.2002.282.1.E207","article-title":"LDL receptor but not apolipoprotein E deficiency in-creases diet-induced obesity and diabetes in mice","volume":"282","author":"SA Schreyer","year":"2002","journal-title":"Am J Physiol Endocrinol Metab"},{"issue":"2","key":"ref36","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrm1837","article-title":"Critical nodes in signalling pathways: insights into insulin action","volume":"7","author":"CM Taniguchi","year":"2006","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"7","key":"ref37","doi-asserted-by":"crossref","first-page":"e6189","DOI":"10.1371\/journal.pone.0006189","article-title":"Insulin stimulates adipogenesis through the Akt-TSC2-mTORC1 pathway","volume":"4","author":"HH Zhang","year":"2009","journal-title":"PLoS One"},{"issue":"10","key":"ref38","doi-asserted-by":"crossref","first-page":"C879","DOI":"10.1152\/ajpcell.00069.2014","article-title":"Signal transduction meets vesicle traffic: the software and hardware of GLUT4 translocation","volume":"306","author":"A Klip","year":"2014","journal-title":"Am J Physiol Cell Physiol"},{"issue":"35","key":"ref39","doi-asserted-by":"crossref","first-page":"4891","DOI":"10.1038\/sj.onc.1203080","article-title":"Identification of a chromosome 3p14.3\u201321.1 gene, APPL, encoding an adaptor molecule that interacts with the oncoprotein-serine\/threonine kinase AKT2","volume":"18","author":"Y Mitsuuchi","year":"1999","journal-title":"Oncogene"},{"issue":"3","key":"ref40","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s10048-015-0441-5","article-title":"Genetic ablation of ataxin-2 in-creases several global translation factors in their transcript abundance but decreases translation rate","volume":"16","author":"M Fittschen","year":"2015","journal-title":"Neurogenetics"},{"issue":"5696","key":"ref41","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1126\/science.1105136","article-title":"The ENCODE (ENCyclopedia Of DNA Elements) Project","volume":"306","author":"EP Consortium","year":"2004","journal-title":"Science"},{"issue":"4","key":"ref42","doi-asserted-by":"crossref","first-page":"e1001046","DOI":"10.1371\/journal.pbio.1001046","article-title":"A user's guide to the encyclopedia of DNA elements (ENCODE)","volume":"9","author":"EP Consortium","year":"2011","journal-title":"PLoS Biol"},{"issue":"9","key":"ref43","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1136\/gut.2008.158386","article-title":"Expression and localisation of insu-lin receptor substrate 2 in normal intestine and colorectal tumours. Regulation by intestine-specific transcription factor CDX2","volume":"58","author":"S Modica","year":"2009","journal-title":"Gut"},{"issue":"44","key":"ref44","doi-asserted-by":"crossref","first-page":"42394","DOI":"10.1074\/jbc.C200444200","article-title":"SOCS-1 and SOCS-3 block insulin signaling by ubiquitin-mediated degradation of IRS1 and IRS2","volume":"277","author":"L Rui","year":"2002","journal-title":"J Biol Chem"},{"issue":"2","key":"ref45","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1002\/jcp.21201","article-title":"Expression of CLMP, a novel tight junction protein, is mediated via the interaction of GATA with the Kruppel family proteins, KLF4 and Sp1, in mouse TM4 Sertoli cells","volume":"214","author":"KL Sze","year":"2008","journal-title":"J Cell Physiol"},{"issue":"5659","key":"ref46","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1094068","article-title":"Inferring cellular networks using probabilistic graphical models","volume":"303","author":"N. Friedman","year":"2004","journal-title":"Science"},{"issue":"9","key":"ref47","doi-asserted-by":"crossref","first-page":"2533","DOI":"10.1007\/s00125-012-2594-1","article-title":"Activating transcription factor 4 mediates hyperglycae-mia-induced endothelial inflammation and retinal vascular leakage through activation of STAT3 in a mouse model of type 1 diabetes","volume":"55","author":"Y Chen","year":"2012","journal-title":"Diabetologia"},{"issue":"2","key":"ref48","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.cmet.2007.01.005","article-title":"Xanthine oxidoreductase is a regulator of adipogenesis and PPARgamma activity","volume":"5","author":"KJ Cheung","year":"2007","journal-title":"Cell Metab"},{"issue":"11","key":"ref49","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":"ref50","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1146\/annurev.cellbio.16.1.145","article-title":"Molecular regulation of adipogenesis","volume":"16","author":"ED Rosen","year":"2000","journal-title":"Annu Rev Cell Dev Biol"},{"issue":"11","key":"ref51","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1210\/me.2009-0160","article-title":"Minireview: Pref-1: role in adipogenesis and mesenchymal cell fate","volume":"23","author":"HS Sul","year":"2009","journal-title":"Mol Endocrinol"}],"updated-by":[{"DOI":"10.1371\/journal.pone.0207325","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2018,11,7]],"date-time":"2018-11-07T00:00:00Z","timestamp":1541548800000}}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0204100","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T12:41:57Z","timestamp":1589028117000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0204100"}},"subtitle":[],"editor":[{"given":"Chunming","family":"Liu","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,9,21]]},"references-count":51,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2018,9,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0204100","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,9,21]]}}}