{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,19]],"date-time":"2025-05-19T17:26:22Z","timestamp":1747675582904},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"S7","license":[{"start":{"date-parts":[[2019,5,1]],"date-time":"2019-05-01T00:00:00Z","timestamp":1556668800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,5]]},"DOI":"10.1186\/s12859-019-2732-6","type":"journal-article","created":{"date-parts":[[2019,5,1]],"date-time":"2019-05-01T00:03:08Z","timestamp":1556668988000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation"],"prefix":"10.1186","volume":"20","author":[{"given":"Yance","family":"Feng","sequence":"first","affiliation":[]},{"given":"Sheng","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Liang","family":"Li","sequence":"additional","affiliation":[]},{"given":"Lei M.","family":"Li","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,5,1]]},"reference":[{"issue":"1","key":"2732_CR1","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1093\/nar\/27.1.318","volume":"27","author":"T Heinemeyer","year":"1999","unstructured":"Heinemeyer T, Chen X, Karas H, Kel AE, Kel O, Liebich I, et al. Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res. 1999;27(1):318\u201322.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2732_CR2","doi-asserted-by":"publisher","first-page":"D260","DOI":"10.1093\/nar\/gkx1126","volume":"46","author":"A Khan","year":"2017","unstructured":"Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2017;46(D1):D260\u2013D6.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"2732_CR3","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1038\/nrg2641","volume":"10","author":"PJ Park","year":"2009","unstructured":"Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009;10(10):669\u201380.","journal-title":"Nat Rev Genet"},{"issue":"25","key":"2732_CR4","doi-asserted-by":"publisher","first-page":"E4914","DOI":"10.1073\/pnas.1704553114","volume":"114","author":"Z Duren","year":"2017","unstructured":"Duren Z, Chen X, Jiang R, Wang Y, Wong WH. Modeling gene regulation from paired expression and chromatin accessibility data. Proc Natl Acad Sci. 2017;114(25):E4914.","journal-title":"Proc Natl Acad Sci"},{"key":"2732_CR5","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1186\/1471-2105-8-452","volume":"8","author":"C Cheng","year":"2007","unstructured":"Cheng C, Yan X, Sun F, Li LM. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics. 2007;8:452.","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"2732_CR6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0001989","volume":"3","author":"C Cheng","year":"2008","unstructured":"Cheng C, Li LM. Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One. 2008;3(4):e1989.","journal-title":"PLoS One"},{"issue":"3","key":"2732_CR7","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/j.ymeth.2014.01.007","volume":"67","author":"L Wang","year":"2014","unstructured":"Wang L, Meng J, Cao W, Li Q, Qiu Y, Sun B, et al. Induction of apoptosis through ER stress and TP53 in MCF-7 cells by the nanoparticle [Gd@ C82 (OH) 22] n: a systems biology study. Methods. 2014;67(3):394\u2013406.","journal-title":"Methods."},{"issue":"1","key":"2732_CR8","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1093\/bioinformatics\/14.1.48","volume":"14","author":"TL Bailey","year":"1998","unstructured":"Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics. 1998;14(1):48\u201354.","journal-title":"Bioinformatics."},{"key":"2732_CR9","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nature03441","volume":"434","author":"X Xie","year":"2005","unstructured":"Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, et al. Systematic discovery of regulatory motifs in human promoters and 3\u2032 UTRs by comparison of several mammals. Nature. 2005;434:338.","journal-title":"Nature."},{"issue":"16","key":"2732_CR10","doi-asserted-by":"publisher","first-page":"9440","DOI":"10.1073\/pnas.1530509100","volume":"100","author":"JD Storey","year":"2003","unstructured":"Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci. 2003;100(16):9440.","journal-title":"Proc Natl Acad Sci"},{"issue":"43","key":"2732_CR11","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102(43):15545.","journal-title":"Proc Natl Acad Sci"},{"issue":"10","key":"2732_CR12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0001095","volume":"2","author":"C Cheng","year":"2007","unstructured":"Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, Li LM. Significant and systematic expression differentiation in long-lived yeast strains. PLoS One. 2007;2(10):e1095.","journal-title":"PLoS One"},{"issue":"1","key":"2732_CR13","doi-asserted-by":"publisher","first-page":"e13","DOI":"10.1371\/journal.pgen.0040013","volume":"4","author":"M Wei","year":"2008","unstructured":"Wei M, Fabrizio P, Hu J, Ge H, Cheng C, Li L, et al. Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras\/PKA, Tor, and Sch9. PLoS Genet. 2008;4(1):e13.","journal-title":"PLoS Genet"},{"issue":"5","key":"2732_CR14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000467","volume":"5","author":"M Wei","year":"2009","unstructured":"Wei M, Fabrizio P, Madia F, Hu J, Ge H, Li LM, et al. Tor1\/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension. PLoS Genet. 2009;5(5):e1000467.","journal-title":"PLoS Genet"},{"issue":"1","key":"2732_CR15","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/1471-2164-10-110","volume":"10","author":"EM van Schothorst","year":"2009","unstructured":"van Schothorst EM, Flachs P, Franssen-van Hal NL, Kuda O, Bunschoten A, Molthoff J, et al. Induction of lipid oxidation by polyunsaturated fatty acids of marine origin in small intestine of mice fed a high-fat diet. BMC Genomics. 2009;10(1):110.","journal-title":"BMC Genomics"},{"issue":"17","key":"2732_CR16","doi-asserted-by":"publisher","first-page":"5565","DOI":"10.1093\/nar\/gki844","volume":"33","author":"C Cheng","year":"2005","unstructured":"Cheng C, Li LM. Sub-array normalization subject to differentiation. Nucleic Acids Res. 2005;33(17):5565\u201373.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2732_CR17","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1016\/j.csda.2004.04.003","volume":"48","author":"LM Li","year":"2005","unstructured":"Li LM. An algorithm for computing exact least-trimmed squares estimate of simple linear regression with constraints. Computational statistics & data analysis. 2005;48(4):717\u201334.","journal-title":"Computational statistics & data analysis"},{"issue":"1","key":"2732_CR18","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1186\/1471-2105-9-194","volume":"9","author":"H Ge","year":"2008","unstructured":"Ge H, Cheng C, Li LM. A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. BMC bioinformatics. 2008;9(1):194.","journal-title":"BMC bioinformatics"},{"key":"2732_CR19","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/537865","volume":"2014","author":"M Aprile","year":"2014","unstructured":"Aprile M, Ambrosio MR, D'Esposito V, Beguinot F, Formisano P, Costa V, et al. PPARG in human Adipogenesis: differential contribution of canonical transcripts and dominant negative isoforms. PPAR Res. 2014;2014:537865.","journal-title":"PPAR Res"},{"issue":"8","key":"2732_CR20","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1016\/j.bbadis.2011.02.014","volume":"1812","author":"T Varga","year":"2011","unstructured":"Varga T, Czimmerer Z, Nagy L. PPARs are a unique set of fatty acid regulated transcription factors controlling both lipid metabolism and inflammation. Biochim Biophys Acta (BBA) - Mol Basis Dis. 2011;1812(8):1007\u201322.","journal-title":"Biochim Biophys Acta (BBA) - Mol Basis Dis"},{"issue":"24","key":"2732_CR21","doi-asserted-by":"publisher","first-page":"7432","DOI":"10.1093\/emboj\/16.24.7432","volume":"16","author":"T Tanaka","year":"1997","unstructured":"Tanaka T, Yoshida N, Kishimoto T, Akira S. Defective adipocyte differentiation in mice lacking the C\/EBPbeta and\/or C\/EBPdelta gene. EMBO J. 1997;16(24):7432\u201343.","journal-title":"EMBO J"},{"issue":"9","key":"2732_CR22","doi-asserted-by":"publisher","first-page":"1538","DOI":"10.1101\/gad.5.9.1538","volume":"5","author":"Z Cao","year":"1991","unstructured":"Cao Z, Umek RM, McKnight SL. Regulated expression of three C\/EBP isoforms during adipose conversion of 3T3-L1 cells. Genes Dev. 1991;5(9):1538\u201352.","journal-title":"Genes Dev"},{"key":"2732_CR23","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1101\/gad.9.2.168","volume":"9","author":"WC Yeh","year":"1995","unstructured":"Yeh WC, Cao ZD, Classon M, McKnight S. Cascade regulation of terminal adipocyte differentiation by three members of the C\/EBP family of leucine zipper proteins. Genes Dev. 1995;9:168\u201381.","journal-title":"Genes Dev"},{"issue":"12","key":"2732_CR24","doi-asserted-by":"publisher","first-page":"3258","DOI":"10.1194\/jlr.M034942","volume":"54","author":"R Kimura","year":"2013","unstructured":"Kimura R, Takahashi N, Lin S, Goto T, Murota K, Nakata R, et al. DHA attenuates postprandial hyperlipidemia via activating PPAR\u03b1 in intestinal epithelial cells. J Lipid Res. 2013;54(12):3258\u201368.","journal-title":"J Lipid Res"},{"issue":"9","key":"2732_CR25","doi-asserted-by":"publisher","first-page":"1936","DOI":"10.1161\/01.ATV.0000232542.42968.e3","volume":"26","author":"A Hamik","year":"2006","unstructured":"Hamik A, Wang B, Jain MK. Transcriptional regulators of angiogenesis. Arterioscler Thromb Vasc Biol. 2006;26(9):1936\u201347.","journal-title":"Arterioscler Thromb Vasc Biol"},{"issue":"6","key":"2732_CR26","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/nm0603-653","volume":"9","author":"P Carmeliet","year":"2003","unstructured":"Carmeliet P. Angiogenesis in health and disease. Nat Med. 2003;9(6):653.","journal-title":"Nat Med"},{"issue":"1","key":"2732_CR27","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1247\/csf.26.19","volume":"26","author":"Y Sato","year":"2001","unstructured":"Sato Y. Role of ETS family transcription factors in vascular development and angiogenesis. Cell Struct Funct. 2001;26(1):19\u201324.","journal-title":"Cell Struct Funct"},{"issue":"6","key":"2732_CR28","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.1042\/BST0371248","volume":"37","author":"M Randi Anna","year":"2009","unstructured":"Randi Anna M, Sperone A, Dryden Nicola H, Birdsey Graeme M. Regulation of angiogenesis by ETS transcription factors. Biochem Soc Trans. 2009;37(6):1248.","journal-title":"Biochem Soc Trans"},{"issue":"1","key":"2732_CR29","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1007\/s12020-013-9941-y","volume":"45","author":"CM Mej\u00eda-Barradas","year":"2014","unstructured":"Mej\u00eda-Barradas CM, Del-R\u00edo-Navarro BE, Dom\u00ednguez-L\u00f3pez A, Campos-Rodr\u00edguez R, Mart\u00ednez-God\u00ednez M-l-\u00c1, Rojas-Hern\u00e1ndez S, et al. The consumption of n-3 polyunsaturated fatty acids differentially modulates gene expression of peroxisome proliferator-activated receptor alpha and gamma and hypoxia-inducible factor 1 alpha in subcutaneous adipose tissue of obese adolescents. Endocrine. 2014;45(1):98\u2013105.","journal-title":"Endocrine."},{"issue":"6","key":"2732_CR30","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1101\/gad.14.6.679","volume":"14","author":"JA Ripperger","year":"2000","unstructured":"Ripperger JA, Shearman LP, Reppert SM, Schibler U. CLOCK, an essential pacemaker component, controls expression of the circadian transcription factor DBP. Genes Dev. 2000;14(6):679\u201389.","journal-title":"Genes Dev"},{"issue":"4","key":"2732_CR31","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1016\/j.neuron.2004.07.018","volume":"43","author":"TK Sato","year":"2004","unstructured":"Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, McNamara P, et al. A functional genomics strategy reveals Rora as a component of the mammalian circadian Clock. Neuron. 2004;43(4):527\u201337.","journal-title":"Neuron."},{"issue":"3","key":"2732_CR32","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1007\/s10695-018-0470-8","volume":"44","author":"Shuqi Wang","year":"2018","unstructured":"Wang S, Chen J, Jiang D, Zhang Q, You C, Tocher D, et al. Hnf4\u03b1 is involved in the regulation of vertebrate LC-PUFA biosynthesis: insights into the regulatory role of Hnf4\u03b1 on expression of liver fatty acyl desaturases in the marine teleost Siganus canaliculatus. Fish Physiol Biochem. 2018;44.","journal-title":"Fish Physiology and Biochemistry"},{"issue":"9","key":"2732_CR33","doi-asserted-by":"publisher","first-page":"2444S","DOI":"10.1093\/jn\/134.9.2444S","volume":"134","author":"J-P P\u00e9gorier","year":"2004","unstructured":"P\u00e9gorier J-P, May CL, Girard J. Control of gene expression by fatty acids. J Nutr. 2004;134(9):2444S\u20139S.","journal-title":"J Nutr"},{"issue":"9","key":"2732_CR34","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1038\/nbt.2957","volume":"32","author":"Consortium SM-I","year":"2014","unstructured":"Consortium SM-I. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium. Nat Biotechnol. 2014;32(9):903\u201314.","journal-title":"Nat Biotechnol"},{"issue":"2","key":"2732_CR35","doi-asserted-by":"crossref","first-page":"115","DOI":"10.33549\/physiolres.930744","volume":"55","author":"M Haluzik","year":"2006","unstructured":"Haluzik M, Haluzik M. PPAR-alpha and insulin sensitivity. Physiol Res. 2006;55(2):115.","journal-title":"Physiol Res"},{"issue":"2","key":"2732_CR36","doi-asserted-by":"publisher","first-page":"E287","DOI":"10.1152\/ajpendo.00440.2004","volume":"288","author":"U Kintscher","year":"2005","unstructured":"Kintscher U, Law RE. PPAR\u03b3-mediated insulin sensitization: the importance of fat versus muscle. American Journal of Physiology-Endocrinology and Metabolism. 2005;288(2):E287\u2013E91.","journal-title":"American Journal of Physiology-Endocrinology and Metabolism"},{"issue":"1","key":"2732_CR37","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/1475-2891-13-17","volume":"13","author":"B Grygiel-G\u00f3rniak","year":"2014","unstructured":"Grygiel-G\u00f3rniak B. Peroxisome proliferator-activated receptors and their ligands: nutritional and clinical implications-a review. Nutr J. 2014;13(1):17.","journal-title":"Nutr J"},{"key":"2732_CR38","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1038\/pr.2015.154","volume":"78","author":"V Wijendran","year":"2015","unstructured":"Wijendran V, Brenna JT, Wang DH, Zhu W, Meng D, Ganguli K, et al. Long-chain polyunsaturated fatty acids attenuate the IL-1\u03b2-induced proinflammatory response in human fetal intestinal epithelial cells. Pediatr Res. 2015;78:626.","journal-title":"Pediatr Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2732-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2732-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2732-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,17]],"date-time":"2022-09-17T06:17:31Z","timestamp":1663395451000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2732-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5]]},"references-count":38,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2019,5]]}},"alternative-id":["2732"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2732-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5]]},"assertion":[{"value":"1 May 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"201"}}