{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T15:15:21Z","timestamp":1676474121932},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"S5","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1752-0509-8-s5-s2","type":"journal-article","created":{"date-parts":[[2014,12,12]],"date-time":"2014-12-12T12:07:43Z","timestamp":1418386063000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Identifying cooperative transcription factors in yeast using multiple data sources"],"prefix":"10.1186","volume":"8","author":[{"given":"Fu-Jou","family":"Lai","sequence":"first","affiliation":[]},{"given":"Mei-Huei","family":"Jhu","sequence":"additional","affiliation":[]},{"given":"Chia-Chun","family":"Chiu","sequence":"additional","affiliation":[]},{"given":"Yueh-Min","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Wei-Sheng","family":"Wu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,12,12]]},"reference":[{"issue":"3","key":"1401_CR1","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1093\/nar\/gkj487","volume":"34","author":"X Yu","year":"2006","unstructured":"Yu X, Lin J, Masuda T, Esumi N, Zack DJ, Qian J: Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res. 2006, 34 (3): 917-927. 10.1093\/nar\/gkj487.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"1401_CR2","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1093\/bioinformatics\/btm523","volume":"24","author":"D Datta","year":"2008","unstructured":"Datta D, Zhao H: Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics. 2008, 24 (4): 545-552. 10.1093\/bioinformatics\/btm523.","journal-title":"Bioinformatics"},{"issue":"5","key":"1401_CR3","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1093\/bioinformatics\/bts002","volume":"28","author":"MJM Chen","year":"2012","unstructured":"Chen MJM, Chou LC, Hsieh TT, Lee DD, Liu KW, Yu CY, Oyang YJ, Tsai HK, Chen CY: De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae. Bioinformatics. 2012, 28 (5): 701-708. 10.1093\/bioinformatics\/bts002.","journal-title":"Bioinformatics"},{"issue":"23","key":"1401_CR4","doi-asserted-by":"publisher","first-page":"7024","DOI":"10.1093\/nar\/gkg894","volume":"31","author":"N Banerjee","year":"2003","unstructured":"Banerjee N, Zhang MQ: Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res. 2003, 31 (23): 7024-7031. 10.1093\/nar\/gkg894.","journal-title":"Nucleic Acids Res"},{"issue":"38","key":"1401_CR5","doi-asserted-by":"publisher","first-page":"13532","DOI":"10.1073\/pnas.0505874102","volume":"102","author":"HK Tsai","year":"2005","unstructured":"Tsai HK, Lu HHS, Li WH: Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci USA. 2005, 102 (38): 13532-13537. 10.1073\/pnas.0505874102.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1401_CR6","first-page":"357","volume-title":"Proceedings of the Fifth International Conference on Grid and Cooperative Computing Workshops","author":"D He","year":"2006","unstructured":"He D, Zhou D, Zhou Y: Identifying synergistic transcriptional factors involved in the yeast cell cycle using microarray and ChIP-chip data. Proceedings of the Fifth International Conference on Grid and Cooperative Computing Workshops. 2006, GCCW '06, Washington, DC, USA: IEEE Computer Society, 357-360."},{"issue":"18","key":"1401_CR7","doi-asserted-by":"publisher","first-page":"2276","DOI":"10.1093\/bioinformatics\/btl380","volume":"22","author":"YH Chang","year":"2006","unstructured":"Chang YH, Wang YC, Chen BS: Identification of transcription factor cooperativity via stochastic system model. Bioinformatics. 2006, 22 (18): 2276-2282. 10.1093\/bioinformatics\/btl380.","journal-title":"Bioinformatics"},{"issue":"15","key":"1401_CR8","doi-asserted-by":"publisher","first-page":"4828","DOI":"10.1093\/nar\/gki793","volume":"33","author":"N Nagamine","year":"2005","unstructured":"Nagamine N, Kawada Y, Sakakibara Y: Identifying cooperative transcriptional regulations using protein-protein interactions. Nucleic Acids Res. 2005, 33 (15): 4828-4837. 10.1093\/nar\/gki793.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"1401_CR9","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1038\/cr.2010.146","volume":"20","author":"Y Yang","year":"2010","unstructured":"Yang Y, Zhang Z, Li Y, Zhu XG, Liu Q: Identifying cooperative transcription factors by combining ChIP-chip data and knockout data. Cell Res. 2010, 20 (11): 1276-1278. 10.1038\/cr.2010.146.","journal-title":"Cell Res"},{"issue":"2","key":"1401_CR10","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/ng724","volume":"29","author":"Y Pilpel","year":"2001","unstructured":"Pilpel Y, Sudarsanam P, Church GM: Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet. 2001, 29 (2): 153-159. 10.1038\/ng724.","journal-title":"Nat Genet"},{"issue":"18","key":"1401_CR11","doi-asserted-by":"publisher","first-page":"5943","DOI":"10.1093\/nar\/gkp625","volume":"37","author":"Y Wang","year":"2009","unstructured":"Wang Y, Zhang XS, Xia Y: Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res. 2009, 37 (18): 5943-5958. 10.1093\/nar\/gkp625.","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"1401_CR12","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1093\/bioinformatics\/btt596","volume":"30","author":"P Hu","year":"2014","unstructured":"Hu P, Shen Z, Tu H, Zhang L, Shi T: Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach. Bioinformatics. 2014, 30 (6): 823-830. 10.1093\/bioinformatics\/btt596.","journal-title":"Bioinformatics"},{"key":"1401_CR13","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1186\/1471-2164-9-332","volume":"9","author":"F Daenen","year":"2008","unstructured":"Daenen F, Van Roy F, De Bleser PJ: Low nucleosome occupancy is encoded around functional human transcription factor binding sites. BMC Genomics. 2008, 9: 332-10.1186\/1471-2164-9-332.","journal-title":"BMC Genomics"},{"key":"1401_CR14","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1186\/1471-2164-11-581","volume":"11","author":"Z Lin","year":"2010","unstructured":"Lin Z, Wu WS, Liang H, Woo Y, Li WH: The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation. BMC Genomics. 2010, 11: 581-10.1186\/1471-2164-11-581.","journal-title":"BMC Genomics"},{"issue":"9","key":"1401_CR15","doi-asserted-by":"publisher","first-page":"e12495","DOI":"10.1371\/journal.pone.0012495","volume":"5","author":"X Yi","year":"2010","unstructured":"Yi X, Cai YD, He Z, Cui W, Kong X: Prediction of nucleosome positioning based on transcription factor binding sites. PLoS One. 2010, 5 (9): e12495-10.1371\/journal.pone.0012495.","journal-title":"PLoS One"},{"key":"1401_CR16","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1186\/1471-2148-11-150","volume":"11","author":"K Swamy","year":"2011","unstructured":"Swamy K, Chu WY, Wang CY, Tsai HK, Wang D: Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast. BMC Evol Biol. 2011, 11: 150-10.1186\/1471-2148-11-150.","journal-title":"BMC Evol Biol"},{"issue":"7","key":"1401_CR17","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1101\/gr.078261.108","volume":"18","author":"TN Mavrich","year":"2008","unstructured":"Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF: A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 2008, 18 (7): 1073-1083. 10.1101\/gr.078261.108.","journal-title":"Genome Res"},{"issue":"suppl 1","key":"1401_CR18","doi-asserted-by":"publisher","first-page":"D136","DOI":"10.1093\/nar\/gkq964","volume":"39","author":"D Abdulrehman","year":"2011","unstructured":"Abdulrehman D, Monteiro PT, Teixeira MC, Mira NP, Louren\u00b8co AB, dos Santos SC, Cabrito TR, Francisco AP, Madeira SC, Aires RS, Oliveira AL, S\u00e1-Correia I, Freitas AT: YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res. 2011, 39 (suppl 1): D136-D140.","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"1401_CR19","doi-asserted-by":"publisher","first-page":"D127","DOI":"10.1093\/nar\/gkl857","volume":"35","author":"M Pachkov","year":"2007","unstructured":"Pachkov M, Erb I, Molina N, Van Nimwegen E: SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res. 2007, 35 (suppl 1): D127-D131.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1401_CR20","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1093\/nar\/gki166","volume":"33","author":"Y Garten","year":"2005","unstructured":"Garten Y, Kaplan S, Pilpel Y: Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data. Nucleic Acids Res. 2005, 33 (2): 605-615. 10.1093\/nar\/gki166.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"1401_CR21","doi-asserted-by":"publisher","first-page":"R62","DOI":"10.1186\/gb-2004-5-9-r62","volume":"5","author":"BE Bernstein","year":"2004","unstructured":"Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL: Global nucleosome occupancy in yeast. Genome Biol. 2004, 5 (9): R62-10.1186\/gb-2004-5-9-r62.","journal-title":"Genome Biol"},{"key":"1401_CR22","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1186\/1471-2105-9-522","volume":"9","author":"WS Wu","year":"2008","unstructured":"Wu WS, Li WH: Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics. 2008, 9: 522-10.1186\/1471-2105-9-522.","journal-title":"BMC Bioinformatics"},{"key":"1401_CR23","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1186\/1752-0509-6-102","volume":"6","author":"TH Yang","year":"2012","unstructured":"Yang TH, Wu WS: Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. BMC Syst Biol. 2012, 6: 102-10.1186\/1752-0509-6-102.","journal-title":"BMC Syst Biol"},{"key":"1401_CR24","doi-asserted-by":"crossref","unstructured":"Lai F, Chang H, Huang Y, Wu W: A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Bio. 8 (S4): S9-","DOI":"10.1186\/1752-0509-8-S4-S9"},{"issue":"suppl 1","key":"1401_CR25","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkj109","volume":"34","author":"C Stark","year":"2006","unstructured":"Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006, 34 (suppl 1): D535-D539.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"1401_CR26","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1093\/bioinformatics\/bts129","volume":"28","author":"H Yang","year":"2012","unstructured":"Yang H, Nepusz T, Paccanaro A: Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. Bioinformatics. 2012, 28 (10): 1383-1389. 10.1093\/bioinformatics\/bts129.","journal-title":"Bioinformatics"},{"key":"1401_CR27","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/nar\/30.1.31","volume":"30","author":"HW Mewes","year":"2002","unstructured":"Mewes HW, Frishman D, G\u00fcldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, M\u00fcnsterk\u00f6tter M, Rudd S, Weil B: MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2002, 30: 31-34. 10.1093\/nar\/30.1.31.","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"1401_CR28","doi-asserted-by":"publisher","first-page":"2407","DOI":"10.1093\/bioinformatics\/btm352","volume":"23","author":"M Elati","year":"2007","unstructured":"Elati M, Neuvial P, Bolotin-Fukuhara M, Barillot E, Radvanyi F, Rouveirol C: LICORN: learning cooperative regulation networks from gene expression data. Bioinformatics. 2007, 23 (18): 2407-2414. 10.1093\/bioinformatics\/btm352.","journal-title":"Bioinformatics"},{"key":"1401_CR29","volume-title":"Database (Oxford)","author":"TH Yang","year":"2014","unstructured":"Yang TH, Wang CC, Wang YC, Wu WS: YTRP: a repository for yeast transcriptional regulatory pathways. Database (Oxford). 2014"},{"issue":"6819","key":"1401_CR30","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/35054095","volume":"409","author":"VR Iyer","year":"2001","unstructured":"Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001, 409 (6819): 533-538. 10.1038\/35054095.","journal-title":"Nature"},{"issue":"5128","key":"1401_CR31","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1126\/science.8372350","volume":"261","author":"C Koch","year":"1993","unstructured":"Koch C, Moll T, Neuberg M, Ahorn H, Nasmyth K: A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science. 1993, 261 (5128): 1551-1557. 10.1126\/science.8372350.","journal-title":"Science"},{"issue":"14","key":"1401_CR32","doi-asserted-by":"publisher","first-page":"5064","DOI":"10.1128\/MCB.23.14.5064-5077.2003","volume":"23","author":"M Costanzo","year":"2003","unstructured":"Costanzo M, Schub O, Andrews B: G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol. 2003, 23 (14): 5064-5077. 10.1128\/MCB.23.14.5064-5077.2003.","journal-title":"Mol Cell Biol"},{"issue":"6791","key":"1401_CR33","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/35017589","volume":"406","author":"M Koranda","year":"2000","unstructured":"Koranda M, Schleiffer A, Endler L, Ammerer G: Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2\/M-specific promoters. Nature. 2000, 406 (6791): 94-98. 10.1038\/35017589.","journal-title":"Nature"},{"issue":"15","key":"1401_CR34","doi-asserted-by":"publisher","first-page":"896","DOI":"10.1016\/S0960-9822(00)00618-7","volume":"10","author":"R Kumar","year":"2000","unstructured":"Kumar R, Reynolds DM, Shevchenko A, Shevchenko A, Goldstone SD, Dalton S: Forkhead transcription factors, Fkh1p and Fkh2p, collaborate with Mcm1p to control transcription required for M-phase. Curr Biol. 2000, 10 (15): 896-906. 10.1016\/S0960-9822(00)00618-7.","journal-title":"Curr Biol"},{"issue":"14","key":"1401_CR35","doi-asserted-by":"publisher","first-page":"3750","DOI":"10.1093\/emboj\/19.14.3750","volume":"19","author":"A Pic","year":"2000","unstructured":"Pic A, Lim FL, Ross SJ, Veal EA, Johnson AL, Sultan MR, West AG, Johnston LH, Sharrocks AD, Morgan BA: The forkhead protein Fkh2 is a component of the yeast cell cycle transcription factor SFF. EMBO J. 2000, 19 (14): 3750-3761. 10.1093\/emboj\/19.14.3750.","journal-title":"EMBO J"},{"issue":"6","key":"1401_CR36","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1016\/S0955-0674(02)00391-5","volume":"14","author":"B Futcher","year":"2002","unstructured":"Futcher B: Transcriptional regulatory networks and the yeast cell cycle. Curr Opin Cell Biol. 2002, 14 (6): 676-683. 10.1016\/S0955-0674(02)00391-5.","journal-title":"Curr Opin Cell Biol"},{"issue":"2","key":"1401_CR37","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1046\/j.1365-2958.2001.02388.x","volume":"40","author":"MT Doolin","year":"2001","unstructured":"Doolin MT, Johnson AL, Johnston LH, Butler G: Overlapping and distinct roles of the duplicated yeast transcription factors Ace2p and Swi5p. Mol Microbiol. 2001, 40 (2): 422-432. 10.1046\/j.1365-2958.2001.02388.x.","journal-title":"Mol Microbiol"},{"issue":"6","key":"1401_CR38","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1016\/j.jbi.2007.02.003","volume":"40","author":"J Wang","year":"2007","unstructured":"Wang J: A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle. J Biomed Inform. 2007, 40 (6): 707-725. 10.1016\/j.jbi.2007.02.003.","journal-title":"J Biomed Inform"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-8-S5-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T19:47:32Z","timestamp":1630612052000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-8-S5-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12]]},"references-count":38,"journal-issue":{"issue":"S5","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["1401"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-8-s5-s2","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12]]},"assertion":[{"value":"12 December 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S2"}}