{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T07:28:05Z","timestamp":1773300485595,"version":"3.50.1"},"reference-count":87,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,3,8]],"date-time":"2010-03-08T00:00:00Z","timestamp":1268006400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1752-0509-4-20","type":"journal-article","created":{"date-parts":[[2012,5,3]],"date-time":"2012-05-03T10:31:46Z","timestamp":1336041106000},"source":"Crossref","is-referenced-by-count":52,"title":["Integrated cellular network of transcription regulations and protein-protein interactions"],"prefix":"10.1186","volume":"4","author":[{"given":"Yu-Chao","family":"Wang","sequence":"first","affiliation":[]},{"given":"Bor-Sen","family":"Chen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,3,8]]},"reference":[{"key":"409_CR1","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/nrm1857","volume":"7","author":"AR Joyce","year":"2006","unstructured":"Joyce AR, Palsson BO: The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol. 2006, 7: 198-210. 10.1038\/nrm1857","journal-title":"Nat Rev Mol Cell Biol"},{"key":"409_CR2","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1038\/msb4100145","volume":"3","author":"T Ideker","year":"2007","unstructured":"Ideker T, Bafna V, Lemberger T: Integrating scientific cultures. Mol Syst Biol. 2007, 3: 105- 10.1038\/msb4100145","journal-title":"Mol Syst Biol"},{"key":"409_CR3","doi-asserted-by":"publisher","first-page":"1914","DOI":"10.1093\/bioinformatics\/bth178","volume":"20","author":"HC Chen","year":"2004","unstructured":"Chen HC, Lee HC, Lin TY, Li WH, Chen BS: Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics. 2004, 20: 1914-1927. 10.1093\/bioinformatics\/bth178","journal-title":"Bioinformatics"},{"key":"409_CR4","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1126\/science.1122088","volume":"312","author":"CT Workman","year":"2006","unstructured":"Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T: A systems approach to mapping DNA damage response pathways. Science. 2006, 312: 1054-1059. 10.1126\/science.1122088","journal-title":"Science"},{"key":"409_CR5","doi-asserted-by":"publisher","first-page":"4007","DOI":"10.1093\/bioinformatics\/bti648","volume":"21","author":"B Xing","year":"2005","unstructured":"Xing B, Laan van der MJ: A causal inference approach for constructing transcriptional regulatory networks. Bioinformatics. 2005, 21: 4007-4013. 10.1093\/bioinformatics\/bti648","journal-title":"Bioinformatics"},{"key":"409_CR6","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1186\/1471-2105-9-228","volume":"9","author":"P Veber","year":"2008","unstructured":"Veber P, Guziolowski C, Le Borgne M, Radulescu O, Siegel A: Inferring the role of transcription factors in regulatory networks. BMC Bioinformatics. 2008, 9: 228- 10.1186\/1471-2105-9-228","journal-title":"BMC Bioinformatics"},{"key":"409_CR7","doi-asserted-by":"publisher","first-page":"1537","DOI":"10.1101\/gr.6202607","volume":"17","author":"S Draghici","year":"2007","unstructured":"Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R: A systems biology approach for pathway level analysis. Genome Res. 2007, 17: 1537-1545. 10.1101\/gr.6202607","journal-title":"Genome Res"},{"key":"409_CR8","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1160\/ME0399","volume":"46","author":"M Visvanathan","year":"2007","unstructured":"Visvanathan M, Breit M, Pfeifer B, Baumgartner C, Modre-Osprian R, Tilg B: Systematic analysis of signaling pathways using an integrative environment. Methods Inf Med. 2007, 46: 386-391.","journal-title":"Methods Inf Med"},{"key":"409_CR9","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/nbt1330","volume":"25","author":"L Kuepfer","year":"2007","unstructured":"Kuepfer L, Peter M, Sauer U, Stelling J: Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol. 2007, 25: 1001-1006. 10.1038\/nbt1330","journal-title":"Nat Biotechnol"},{"key":"409_CR10","doi-asserted-by":"publisher","first-page":"6053","DOI":"10.1093\/nar\/gkg787","volume":"31","author":"E Yeger-Lotem","year":"2003","unstructured":"Yeger-Lotem E, Margalit H: Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. Nucleic Acids Res. 2003, 31: 6053-6061. 10.1093\/nar\/gkg787","journal-title":"Nucleic Acids Res"},{"key":"409_CR11","doi-asserted-by":"publisher","first-page":"5934","DOI":"10.1073\/pnas.0306752101","volume":"101","author":"E Yeger-Lotem","year":"2004","unstructured":"Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter RY, Alon U, Margalit H: Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA. 2004, 101: 5934-5939. 10.1073\/pnas.0306752101","journal-title":"Proc Natl Acad Sci USA"},{"key":"409_CR12","doi-asserted-by":"publisher","first-page":"R35","DOI":"10.1186\/gb-2005-6-4-r35","volume":"6","author":"A Mazurie","year":"2005","unstructured":"Mazurie A, Bottani S, Vergassola M: An evolutionary and functional assessment of regulatory network motifs. Genome Biol. 2005, 6: R35- 10.1186\/gb-2005-6-4-r35","journal-title":"Genome Biol"},{"key":"409_CR13","doi-asserted-by":"publisher","first-page":"i359","DOI":"10.1093\/bioinformatics\/btm170","volume":"23","author":"O Ourfali","year":"2007","unstructured":"Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R: SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics. 2007, 23: i359-366. 10.1093\/bioinformatics\/btm170","journal-title":"Bioinformatics"},{"key":"409_CR14","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1038\/nature04335","volume":"438","author":"D Sprinzak","year":"2005","unstructured":"Sprinzak D, Elowitz MB: Reconstruction of genetic circuits. Nature. 2005, 438: 443-448. 10.1038\/nature04335","journal-title":"Nature"},{"key":"409_CR15","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1038\/nrmicro1949","volume":"7","author":"AM Feist","year":"2009","unstructured":"Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO: Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol. 2009, 7: 129-143.","journal-title":"Nat Rev Microbiol"},{"key":"409_CR16","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: 2276-2282. 10.1093\/bioinformatics\/btl380","journal-title":"Bioinformatics"},{"key":"409_CR17","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","volume":"22","author":"M Bansal","year":"2006","unstructured":"Bansal M, Gatta GD, di Bernardo D: Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics. 2006, 22: 815-822. 10.1093\/bioinformatics\/btl003","journal-title":"Bioinformatics"},{"key":"409_CR18","volume-title":"Mol Syst Biol","author":"M Bansal","year":"2007","unstructured":"Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D: How to infer gene networks from expression profiles. Mol Syst Biol. 2007, 3:"},{"key":"409_CR19","doi-asserted-by":"publisher","first-page":"4241","DOI":"10.1091\/mbc.11.12.4241","volume":"11","author":"AP Gasch","year":"2000","unstructured":"Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000, 11: 4241-4257.","journal-title":"Mol Biol Cell"},{"key":"409_CR20","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nature02800","volume":"431","author":"CT Harbison","year":"2004","unstructured":"Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al.: Transcriptional regulatory code of a eukaryotic genome. Nature. 2004, 431: 99-104. 10.1038\/nature02800","journal-title":"Nature"},{"key":"409_CR21","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/nar\/26.1.73","volume":"26","author":"JM Cherry","year":"1998","unstructured":"Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, et al.: SGD: Saccharomyces Genome Database. Nucl Acids Res. 1998, 26: 73-79. 10.1093\/nar\/26.1.73","journal-title":"Nucl Acids Res"},{"key":"409_CR22","doi-asserted-by":"publisher","first-page":"D446","DOI":"10.1093\/nar\/gkj013","volume":"34","author":"MC Teixeira","year":"2006","unstructured":"Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sa-Correia I: The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 2006, 34: D446-451. 10.1093\/nar\/gkj013","journal-title":"Nucleic Acids Res"},{"key":"409_CR23","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkj109","volume":"34","author":"C Stark","year":"2006","unstructured":"Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucl Acids Res. 2006, 34: D535-539. 10.1093\/nar\/gkj109","journal-title":"Nucl Acids Res"},{"key":"409_CR24","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038\/75556","journal-title":"Nat Genet"},{"key":"409_CR25","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","volume":"19","author":"H Akaike","year":"1974","unstructured":"Akaike H: A new look at the statistical model identification. IEEE Transactions on Automatic Control. 1974, 19: 716-723. 10.1109\/TAC.1974.1100705.","journal-title":"IEEE Transactions on Automatic Control"},{"key":"409_CR26","volume-title":"System modeling and identification","author":"R Johansson","year":"1993","unstructured":"Johansson R: System modeling and identification. 1993, Englewood Cliffs, N.J.: Prentice Hall"},{"key":"409_CR27","volume-title":"Statistics for engineering and the sciences","author":"W Mendenhall","year":"1995","unstructured":"Mendenhall W, Sincich T: Statistics for engineering and the sciences. 1995, Englewood Cliffs, N.J.: Prentice-Hall, 4","edition":"4"},{"key":"409_CR28","doi-asserted-by":"publisher","DOI":"10.1007\/3-540-45611-2","volume-title":"Yeast stress responses","author":"S Hohmann","year":"2003","unstructured":"Hohmann S, Mager WH: Yeast stress responses. 2003, Berlin; New York: Springer"},{"key":"409_CR29","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1186\/1471-2105-8-188","volume":"8","author":"WS Wu","year":"2007","unstructured":"Wu WS, Li WH, Chen BS: Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics. 2007, 8: 188- 10.1186\/1471-2105-8-188","journal-title":"BMC Bioinformatics"},{"key":"409_CR30","volume-title":"An introduction to systems biology: design principles of biological circuits","author":"U Alon","year":"2007","unstructured":"Alon U: An introduction to systems biology: design principles of biological circuits. 2007, Boca Raton, FL: Chapman & Hall\/CRC"},{"key":"409_CR31","doi-asserted-by":"publisher","first-page":"2883","DOI":"10.1093\/bioinformatics\/bti415","volume":"21","author":"KC Chen","year":"2005","unstructured":"Chen KC, Wang TY, Tseng HH, Huang CY, Kao CY: A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics. 2005, 21: 2883-2890. 10.1093\/bioinformatics\/bti415","journal-title":"Bioinformatics"},{"key":"409_CR32","first-page":"53","volume":"2","author":"WS Wu","year":"2008","unstructured":"Wu WS, Li WH, Chen BS: Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. Gene Regulation and Systems Biology. 2008, 2: 53-62.","journal-title":"Gene Regulation and Systems Biology"},{"key":"409_CR33","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1089\/10665270252833208","volume":"9","author":"H de Jong","year":"2002","unstructured":"de Jong H: Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol. 2002, 9: 67-103. 10.1089\/10665270252833208","journal-title":"J Comput Biol"},{"key":"409_CR34","doi-asserted-by":"publisher","first-page":"5944","DOI":"10.1073\/pnas.0933416100","volume":"100","author":"J Tegner","year":"2003","unstructured":"Tegner J, Yeung MK, Hasty J, Collins JJ: Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci USA. 2003, 100: 5944-5949. 10.1073\/pnas.0933416100","journal-title":"Proc Natl Acad Sci USA"},{"key":"409_CR35","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1126\/science.287.5454.873","volume":"287","author":"CJ Roberts","year":"2000","unstructured":"Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, et al.: Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science. 2000, 287: 873-880. 10.1126\/science.287.5454.873","journal-title":"Science"},{"key":"409_CR36","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/1471-2105-3-34","volume":"3","author":"M Steffen","year":"2002","unstructured":"Steffen M, Petti A, Aach J, D'Haeseleer P, Church G: Automated modelling of signal transduction networks. BMC Bioinformatics. 2002, 3: 34- 10.1186\/1471-2105-3-34","journal-title":"BMC Bioinformatics"},{"key":"409_CR37","doi-asserted-by":"publisher","first-page":"7165","DOI":"10.1073\/pnas.0710770105","volume":"105","author":"P Hersen","year":"2008","unstructured":"Hersen P, McClean MN, Mahadevan L, Ramanathan S: Signal processing by the HOG MAP kinase pathway. Proc Natl Acad Sci USA. 2008, 105: 7165-7170. 10.1073\/pnas.0710770105","journal-title":"Proc Natl Acad Sci USA"},{"key":"409_CR38","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1126\/science.7624781","volume":"269","author":"T Maeda","year":"1995","unstructured":"Maeda T, Takekawa M, Saito H: Activation of yeast PBS2 MAPKK by MAPKKKs or by binding of an SH3-containing osmosensor. Science. 1995, 269: 554-558. 10.1126\/science.7624781","journal-title":"Science"},{"key":"409_CR39","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1016\/S0092-8674(00)80162-2","volume":"86","author":"F Posas","year":"1996","unstructured":"Posas F, Wurgler-Murphy SM, Maeda T, Witten EA, Thai TC, Saito H: Yeast HOG1 MAP kinase cascade is regulated by a multistep phosphorelay mechanism in the SLN1-YPD1-SSK1 \"two-component\" osmosensor. Cell. 1996, 86: 865-875. 10.1016\/S0092-8674(00)80162-2","journal-title":"Cell"},{"key":"409_CR40","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1093\/emboj\/17.5.1385","volume":"17","author":"F Posas","year":"1998","unstructured":"Posas F, Saito H: Activation of the yeast SSK2 MAP kinase kinase kinase by the SSK1 two-component response regulator. EMBO J. 1998, 17: 1385-1394. 10.1093\/emboj\/17.5.1385","journal-title":"EMBO J"},{"key":"409_CR41","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/369242a0","volume":"369","author":"T Maeda","year":"1994","unstructured":"Maeda T, Wurgler-Murphy SM, Saito H: A two-component system that regulates an osmosensing MAP kinase cascade in yeast. Nature. 1994, 369: 242-245. 10.1038\/369242a0","journal-title":"Nature"},{"key":"409_CR42","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1126\/science.7681220","volume":"259","author":"JL Brewster","year":"1993","unstructured":"Brewster JL, de Valoir T, Dwyer ND, Winter E, Gustin MC: An osmosensing signal transduction pathway in yeast. Science. 1993, 259: 1760-1763. 10.1126\/science.7681220","journal-title":"Science"},{"key":"409_CR43","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1038\/35023568","volume":"2","author":"V Reiser","year":"2000","unstructured":"Reiser V, Salah SM, Ammerer G: Polarized localization of yeast Pbs2 depends on osmostress, the membrane protein Sho1 and Cdc42. Nat Cell Biol. 2000, 2: 620-627. 10.1038\/35023568","journal-title":"Nat Cell Biol"},{"key":"409_CR44","doi-asserted-by":"publisher","first-page":"4623","DOI":"10.1093\/emboj\/19.17.4623","volume":"19","author":"DC Raitt","year":"2000","unstructured":"Raitt DC, Posas F, Saito H: Yeast Cdc42 GTPase and Ste20 PAK-like kinase regulate Sho1-dependent activation of the Hog1 MAPK pathway. EMBO J. 2000, 19: 4623-4631. 10.1093\/emboj\/19.17.4623","journal-title":"EMBO J"},{"key":"409_CR45","doi-asserted-by":"publisher","first-page":"5788","DOI":"10.1128\/MCB.18.10.5788","volume":"18","author":"F Posas","year":"1998","unstructured":"Posas F, Witten EA, Saito H: Requirement of STE50 for osmostress-induced activation of the STE11 mitogen-activated protein kinase kinase kinase in the high-osmolarity glycerol response pathway. Mol Cell Biol. 1998, 18: 5788-5796.","journal-title":"Mol Cell Biol"},{"key":"409_CR46","doi-asserted-by":"publisher","first-page":"4739","DOI":"10.1128\/MCB.22.13.4739-4749.2002","volume":"22","author":"SM O'Rourke","year":"2002","unstructured":"O'Rourke SM, Herskowitz I: A third osmosensing branch in Saccharomyces cerevisiae requires the Msb2 protein and functions in parallel with the Sho1 branch. Mol Cell Biol. 2002, 22: 4739-4749. 10.1128\/MCB.22.13.4739-4749.2002","journal-title":"Mol Cell Biol"},{"key":"409_CR47","doi-asserted-by":"publisher","first-page":"3521","DOI":"10.1038\/sj.emboj.7601796","volume":"26","author":"K Tatebayashi","year":"2007","unstructured":"Tatebayashi K, Tanaka K, Yang HY, Yamamoto K, Matsushita Y, Tomida T, Imai M, Saito H: Transmembrane mucins Hkr1 and Msb2 are putative osmosensors in the SHO1 branch of yeast HOG pathway. EMBO J. 2007, 26: 3521-3533. 10.1038\/sj.emboj.7601796","journal-title":"EMBO J"},{"key":"409_CR48","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1091\/mbc.10.4.1147","volume":"10","author":"V Reiser","year":"1999","unstructured":"Reiser V, Ruis H, Ammerer G: Kinase activity-dependent nuclear export opposes stress-induced nuclear accumulation and retention of Hog1 mitogen-activated protein kinase in the budding yeast Saccharomyces cerevisiae. Mol Biol Cell. 1999, 10: 1147-1161.","journal-title":"Mol Biol Cell"},{"key":"409_CR49","doi-asserted-by":"publisher","first-page":"5606","DOI":"10.1093\/emboj\/17.19.5606","volume":"17","author":"P Ferrigno","year":"1998","unstructured":"Ferrigno P, Posas F, Koepp D, Saito H, Silver PA: Regulated nucleo\/cytoplasmic exchange of HOG1 MAPK requires the importin beta homologs NMD5 and XPO1. EMBO J. 1998, 17: 5606-5614. 10.1093\/emboj\/17.19.5606","journal-title":"EMBO J"},{"key":"409_CR50","doi-asserted-by":"publisher","first-page":"5625","DOI":"10.1073\/pnas.091610798","volume":"98","author":"M Teige","year":"2001","unstructured":"Teige M, Scheikl E, Reiser V, Ruis H, Ammerer G: Rck2, a member of the calmodulin-protein kinase family, links protein synthesis to high osmolarity MAP kinase signaling in budding yeast. Proc Natl Acad Sci USA. 2001, 98: 5625-5630. 10.1073\/pnas.091610798","journal-title":"Proc Natl Acad Sci USA"},{"key":"409_CR51","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1101\/gad.14.10.1229","volume":"14","author":"CP Mattison","year":"2000","unstructured":"Mattison CP, Ota IM: Two protein tyrosine phosphatases, Ptp2 and Ptp3, modulate the subcellular localization of the Hog1 MAP kinase in yeast. Genes Dev. 2000, 14: 1229-1235.","journal-title":"Genes Dev"},{"key":"409_CR52","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/nature04187","volume":"438","author":"J Ptacek","year":"2005","unstructured":"Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, et al.: Global analysis of protein phosphorylation in yeast. Nature. 2005, 438: 679-684. 10.1038\/nature04187","journal-title":"Nature"},{"key":"409_CR53","doi-asserted-by":"publisher","first-page":"1032","DOI":"10.1128\/EC.1.6.1032-1040.2002","volume":"1","author":"C Young","year":"2002","unstructured":"Young C, Mapes J, Hanneman J, Al-Zarban S, Ota I: Role of Ptc2 type 2C Ser\/Thr phosphatase in yeast high-osmolarity glycerol pathway inactivation. Eukaryot Cell. 2002, 1: 1032-1040. 10.1128\/EC.1.6.1032-1040.2002","journal-title":"Eukaryot Cell"},{"key":"409_CR54","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1128\/MCB.21.1.51-60.2001","volume":"21","author":"J Warmka","year":"2001","unstructured":"Warmka J, Hanneman J, Lee J, Amin D, Ota I: Ptc1, a type 2C Ser\/Thr phosphatase, inactivates the HOG pathway by dephosphorylating the mitogen-activated protein kinase Hog1. Mol Cell Biol. 2001, 21: 51-60. 10.1128\/MCB.21.1.51-60.2001","journal-title":"Mol Cell Biol"},{"key":"409_CR55","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nrg1272","volume":"5","author":"AL Barabasi","year":"2004","unstructured":"Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004, 5: 101-113. 10.1038\/nrg1272","journal-title":"Nat Rev Genet"},{"key":"409_CR56","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/35075138","volume":"411","author":"H Jeong","year":"2001","unstructured":"Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in protein networks. Nature. 2001, 411: 41-42. 10.1038\/35075138","journal-title":"Nature"},{"key":"409_CR57","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/1755-8794-1-46","volume":"1","author":"BS Chen","year":"2008","unstructured":"Chen BS, Yang SK, Lan CY, Chuang YJ: A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med Genomics. 2008, 1: 46- 10.1186\/1755-8794-1-46","journal-title":"BMC Med Genomics"},{"key":"409_CR58","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1111\/j.1567-1364.2006.00026.x","volume":"6","author":"XX Yang","year":"2006","unstructured":"Yang XX, Maurer KC, Molanus M, Mager WH, Siderius M, Vies van der SM: The molecular chaperone Hsp90 is required for high osmotic stress response in Saccharomyces cerevisiae. FEMS Yeast Res. 2006, 6: 195-204. 10.1111\/j.1567-1364.2006.00026.x","journal-title":"FEMS Yeast Res"},{"key":"409_CR59","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.gde.2004.12.011","volume":"15","author":"LH Pearl","year":"2005","unstructured":"Pearl LH: Hsp90 and Cdc37 -- a chaperone cancer conspiracy. Curr Opin Genet Dev. 2005, 15: 55-61. 10.1016\/j.gde.2004.12.011","journal-title":"Curr Opin Genet Dev"},{"key":"409_CR60","doi-asserted-by":"publisher","first-page":"6232","DOI":"10.1128\/MCB.15.11.6232","volume":"15","author":"J Varela","year":"1995","unstructured":"Varela J, Praekelt U, Meacock P, Planta R, Mager W: The Saccharomyces cerevisiae HSP12 gene is activated by the high-osmolarity glycerol pathway and negatively regulated by protein kinase A. Mol Cell Biol. 1995, 15: 6232-6245.","journal-title":"Mol Cell Biol"},{"key":"409_CR61","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.bbapap.2006.10.009","volume":"1774","author":"RJ Karreman","year":"2007","unstructured":"Karreman RJ, Dague E, Gaboriaud F, Quiles F, Duval JF, Lindsey GG: The stress response protein Hsp12p increases the flexibility of the yeast Saccharomyces cerevisiae cell wall. Biochim Biophys Acta. 2007, 1774: 131-137.","journal-title":"Biochim Biophys Acta"},{"key":"409_CR62","doi-asserted-by":"crossref","first-page":"4382","DOI":"10.1002\/j.1460-2075.1994.tb06758.x","volume":"13","author":"C Schuller","year":"1994","unstructured":"Schuller C, Brewster JL, Alexander MR, Gustin MC, Ruis H: The HOG pathway controls osmotic regulation of transcription via the stress response element (STRE) of the Saccharomyces cerevisiae CTT1 gene. EMBO J. 1994, 13: 4382-4389.","journal-title":"EMBO J"},{"key":"409_CR63","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1002\/j.1460-2075.1993.tb05849.x","volume":"12","author":"G Marchler","year":"1993","unstructured":"Marchler G, Schuller C, Adam G, Ruis H: A Saccharomyces cerevisiae UAS element controlled by protein kinase A activates transcription in response to a variety of stress conditions. EMBO J. 1993, 12: 1997-2003.","journal-title":"EMBO J"},{"key":"409_CR64","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1517\/17460441.2.5.755","volume":"2","author":"BS Chen","year":"2007","unstructured":"Chen BS, Li CW: Analysing microarray data in drug discovery using systems biology. Expert Opinion on Drug Discovery. 2007, 2: 755-768. 10.1517\/17460441.2.5.755.","journal-title":"Expert Opinion on Drug Discovery"},{"key":"409_CR65","doi-asserted-by":"publisher","first-page":"1515","DOI":"10.1002\/yea.779","volume":"18","author":"JA Diderich","year":"2001","unstructured":"Diderich JA, Schuurmans JM, Van Gaalen MC, Kruckeberg AL, Van Dam K: Functional analysis of the hexose transporter homologue HXT5 in Saccharomyces cerevisiae. Yeast. 2001, 18: 1515-1524. 10.1002\/yea.779","journal-title":"Yeast"},{"key":"409_CR66","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1002\/yea.895","volume":"19","author":"R Verwaal","year":"2002","unstructured":"Verwaal R, Paalman JW, Hogenkamp A, Verkleij AJ, Verrips CT, Boonstra J: HXT5 expression is determined by growth rates in Saccharomyces cerevisiae. Yeast. 2002, 19: 1029-1038. 10.1002\/yea.895","journal-title":"Yeast"},{"key":"409_CR67","doi-asserted-by":"publisher","first-page":"3919","DOI":"10.1128\/MCB.9.9.3919","volume":"9","author":"KA Borkovich","year":"1989","unstructured":"Borkovich KA, Farrelly FW, Finkelstein DB, Taulien J, Lindquist S: hsp82 is an essential protein that is required in higher concentrations for growth of cells at higher temperatures. Mol Cell Biol. 1989, 9: 3919-3930.","journal-title":"Mol Cell Biol"},{"key":"409_CR68","doi-asserted-by":"publisher","first-page":"1640","DOI":"10.1007\/PL00012491","volume":"59","author":"D Picard","year":"2002","unstructured":"Picard D: Heat-shock protein 90, a chaperone for folding and regulation. Cell Mol Life Sci. 2002, 59: 1640-1648. 10.1007\/PL00012491","journal-title":"Cell Mol Life Sci"},{"key":"409_CR69","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1016\/j.tibtech.2004.07.007","volume":"22","author":"M Csete","year":"2004","unstructured":"Csete M, Doyle J: Bow ties, metabolism and disease. Trends Biotechnol. 2004, 22: 446-450. 10.1016\/j.tibtech.2004.07.007","journal-title":"Trends Biotechnol"},{"key":"409_CR70","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1007\/s00227-003-1190-9","volume":"144","author":"R Li","year":"2004","unstructured":"Li R, Brawley S: Improved survival under heat stress in intertidal embryos (Fucus spp.) simultaneously exposed to hypersalinity and the effect of parental thermal history. Marine Biology. 2004, 144: 205-213. 10.1007\/s00227-003-1190-9.","journal-title":"Marine Biology"},{"key":"409_CR71","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1104\/pp.119.1.205","volume":"119","author":"L Xiong","year":"1999","unstructured":"Xiong L, Ishitani M, Zhu JK: Interaction of osmotic stress, temperature, and abscisic acid in the regulation of gene expression in Arabidopsis. Plant Physiol. 1999, 119: 205-212. 10.1104\/pp.119.1.205","journal-title":"Plant Physiol"},{"key":"409_CR72","doi-asserted-by":"publisher","first-page":"2856","DOI":"10.1002\/pmic.200700095","volume":"7","author":"S Zhang","year":"2007","unstructured":"Zhang S, Jin G, Zhang XS, Chen L: Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics. 2007, 7: 2856-2869. 10.1002\/pmic.200700095","journal-title":"Proteomics"},{"key":"409_CR73","first-page":"166","volume":"34","author":"E Segal","year":"2003","unstructured":"Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. NatGenet. 2003, 34: 166-176.","journal-title":"NatGenet"},{"key":"409_CR74","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1038\/hdy.2009.18","volume":"102","author":"G Cuccato","year":"2009","unstructured":"Cuccato G, Della Gatta G, di Bernardo D: Systems and Synthetic biology: tackling genetic networks and complex diseases. Heredity. 2009, 102: 527-532. 10.1038\/hdy.2009.18","journal-title":"Heredity"},{"key":"409_CR75","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt.1499","volume":"26","author":"G Chechik","year":"2008","unstructured":"Chechik G, Oh E, Rando O, Weissman J, Regev A, Koller D: Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat Biotechnol. 2008, 26: 1251-1259. 10.1038\/nbt.1499","journal-title":"Nat Biotechnol"},{"key":"409_CR76","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1101\/gr.5321506","volume":"16","author":"AJ Walhout","year":"2006","unstructured":"Walhout AJ: Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res. 2006, 16: 1445-1454. 10.1101\/gr.5321506","journal-title":"Genome Res"},{"key":"409_CR77","doi-asserted-by":"publisher","first-page":"854","DOI":"10.1038\/ng.167","volume":"40","author":"J Zhu","year":"2008","unstructured":"Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE: Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet. 2008, 40: 854-861. 10.1038\/ng.167","journal-title":"Nat Genet"},{"key":"409_CR78","volume-title":"Proceedings of the sixth annual international conference on Computational biology","author":"Z Bar-Joseph","year":"2002","unstructured":"Bar-Joseph Z, Gerber G, Gifford DK, Jaakkola TS, Simon I: A new approach to analyzing gene expression time series data. Proceedings of the sixth annual international conference on Computational biology. 2002, Washington, DC, USA: ACM"},{"key":"409_CR79","volume-title":"Numerical methods","author":"JD Faires","year":"1998","unstructured":"Faires JD, Burden RL: Numerical methods. 1998, Pacific Grove, CA: Brooks\/Cole Pub. Co., 2","edition":"2"},{"key":"409_CR80","volume-title":"A practical guide to splines Rev edn","author":"C de Boor","year":"2001","unstructured":"de Boor C: A practical guide to splines Rev edn. 2001, New York: Springer"},{"key":"409_CR81","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1007\/BF01589112","volume":"45","author":"TF Coleman","year":"1989","unstructured":"Coleman TF, Hulbert LA: A direct active set algorithm for large sparse quadratic programs with simple bounds. Mathematical Programming. 1989, 45: 373-406. 10.1007\/BF01589112.","journal-title":"Mathematical Programming"},{"key":"409_CR82","volume-title":"Practical optimization","author":"PE Gill","year":"1981","unstructured":"Gill PE, Murray W, Wright MH: Practical optimization. 1981, London; New York: Academic Press"},{"key":"409_CR83","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/nbt1270","volume":"25","author":"P Lu","year":"2007","unstructured":"Lu P, Vogel C, Wang R, Yao X, Marcotte EM: Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007, 25: 117-124. 10.1038\/nbt1270","journal-title":"Nat Biotechnol"},{"key":"409_CR84","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2307\/2529336","volume":"32","author":"RR Hocking","year":"1976","unstructured":"Hocking RR: A Biometrics invited paper. The analysis and selection of variables in linear regression. Biometrics. 1976, 32: 1-49. 10.2307\/2529336.","journal-title":"Biometrics"},{"key":"409_CR85","doi-asserted-by":"publisher","DOI":"10.1002\/9780471722199","volume-title":"Linear regression analysis","author":"GAF Seber","year":"2003","unstructured":"Seber GAF, Lee AJ: Linear regression analysis. 2003, Hoboken, N.J.: Wiley-Interscience, 2","edition":"2"},{"key":"409_CR86","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1093\/bioinformatics\/btm057","volume":"23","author":"A Barsky","year":"2007","unstructured":"Barsky A, Gardy JL, Hancock RE, Munzner T: Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics. 2007, 23: 1040-1042. 10.1093\/bioinformatics\/btm057","journal-title":"Bioinformatics"},{"key":"409_CR87","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13: 2498-2504. 10.1101\/gr.1239303","journal-title":"Genome Res"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-20.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-4-20\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-20.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,14]],"date-time":"2022-01-14T20:11:41Z","timestamp":1642191101000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-4-20"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,3,8]]},"references-count":87,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["409"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-4-20","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,3,8]]},"article-number":"20"}}