{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T21:35:48Z","timestamp":1771104948827,"version":"3.50.1"},"reference-count":69,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2013,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Dysregulation of genetic factors such as microRNAs (miRNAs) and mRNAs has been widely shown to be associated with cancer progression and development. In particular, miRNAs and mRNAs cooperate to affect biological processes, including tumorigenesis. The complexity of miRNA-mRNA interactions presents a major barrier to identifying their co-regulatory roles and functional effects. Thus, by computationally modeling these complex relationships, it may be possible to infer the gene interaction networks underlying complicated biological processes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose a data-driven, hypergraph structural method for constructing higher-order miRNA-mRNA interaction networks from cancer genomic profiles. The proposed model explicitly characterizes higher-order relationships among genetic factors, from which cooperative gene activities in biological processes may be identified. The proposed model is learned by iteration of structure and parameter learning. The structure learning efficiently constructs a hypergraph structure by generating putative hyperedges representing complex miRNA-mRNA modules. It adopts an evolutionary method based on information-theoretic criteria. In the parameter learning phase, the constructed hypergraph is refined by updating the hyperedge weights using the gradient descent method. From the model, we produce biologically relevant higher-order interaction networks showing the properties of primary and metastatic prostate cancer, as candidates of potential miRNA-mRNA regulatory circuits.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our approach focuses on potential cancer-specific interactions reflecting higher-order relationships between miRNAs and mRNAs from expression profiles. The constructed miRNA-mRNA interaction networks show oncogenic or tumor suppression characteristics, which are known to be directly associated with prostate cancer progression. Therefore, the hypergraph-based model can assist hypothesis formulation for the molecular pathogenesis of cancer.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1752-0509-7-47","type":"journal-article","created":{"date-parts":[[2013,6,19]],"date-time":"2013-06-19T18:14:33Z","timestamp":1371665673000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning"],"prefix":"10.1186","volume":"7","author":[{"given":"Soo-Jin","family":"Kim","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jung-Woo","family":"Ha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Byoung-Tak","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,6,19]]},"reference":[{"issue":"5","key":"1134_CR1","doi-asserted-by":"publisher","first-page":"277","DOI":"10.3322\/caac.20073","volume":"60","author":"A Jemal","year":"2010","unstructured":"Jemal A, Siegel R, Xu J, Ward E: Cancer statistics, 2010. CA Cancer J Clin. 2010, 60 (5): 277-300, 10.3322\/caac.20073","journal-title":"CA Cancer J Clin"},{"key":"1134_CR2","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/35011540","volume":"402","author":"LH Hartwell","year":"1999","unstructured":"Hartwell LH, Hopfield JJ, Leibler S, Murray AW: From molecular to modular cell biology. Nature. 1999, 402: 47-52. 10.1038\/46972.","journal-title":"Nature"},{"issue":"5","key":"1134_CR3","doi-asserted-by":"publisher","first-page":"e1000385","DOI":"10.1371\/journal.pcbi.1000385","volume":"5","author":"S Klamt","year":"2009","unstructured":"Klamt S, Haus U, Theis F: Hypergraphs and cellular networks. PLoS Comput Biol. 2009, 5 (5): e1000385-10.1371\/journal.pcbi.1000385.","journal-title":"PLoS Comput Biol"},{"key":"1134_CR4","doi-asserted-by":"publisher","first-page":"F1","DOI":"10.1677\/ERC-09-0172","volume":"17","author":"V Coppola","year":"2010","unstructured":"Coppola V, Maria RD, Bonci D: MicroRNAs and prostate cancer. Endocr Relat Cancer. 2010, 17: F1-F17. 10.1677\/ERC-09-0172.","journal-title":"Endocr Relat Cancer"},{"key":"1134_CR5","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1093\/abbs\/gmq038","volume":"42","author":"Y Pang","year":"2010","unstructured":"Pang Y, Young CY, Yuan H: MicroRNAs and prostate cancer. Acta Biochim Biophys Sin. 2010, 42: 363-69. 10.1093\/abbs\/gmq038.","journal-title":"Acta Biochim Biophys Sin"},{"key":"1134_CR6","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1038\/pcan.2012.3","volume":"15","author":"A Gordanpour","year":"2012","unstructured":"Gordanpour A, Nam RK, Sugar L, Seth A: MicroRNAs in prostate cancer: from biomarkers to molecularly-based therapeutics. Prostate Cancer Prostatic Dis. 2012, 15: 314-319. 10.1038\/pcan.2012.3.","journal-title":"Prostate Cancer Prostatic Dis"},{"issue":"9","key":"1134_CR7","doi-asserted-by":"publisher","first-page":"e24950","DOI":"10.1371\/journal.pone.0024950","volume":"6","author":"A Watahiki","year":"2011","unstructured":"Watahiki A, Wang Y, Morris J, Dennis K, O'Dwyer HM, Gleave M, Gout PW, Wang Y: MicroRNAs associated with metastatic prostate cancer. PLoS One. 2011, 6 (9): e24950-10.1371\/journal.pone.0024950.","journal-title":"PLoS One"},{"key":"1134_CR8","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1002\/ijc.24827","volume":"126","author":"A Schaefer","year":"2010","unstructured":"Schaefer A, Jung M, Mollenkopf HJ, Wagner I, Stephan C, Jentzmik F, Miller K, Lein M, Kristiansen G, Jung K: Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma. Int J Cancer. 2010, 126: 1166-1176.","journal-title":"Int J Cancer"},{"key":"1134_CR9","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.biosystems.2005.05.014","volume":"83","author":"JJ Hornberg","year":"2006","unstructured":"Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J: Cancer: a systems biology disease. Biosystems. 2006, 83: 81-90. 10.1016\/j.biosystems.2005.05.014.","journal-title":"Biosystems"},{"issue":"14","key":"1134_CR10","doi-asserted-by":"publisher","first-page":"1752","DOI":"10.1007\/s00018-007-7054-6","volume":"64","author":"E Wang","year":"2007","unstructured":"Wang E, Lenferink A, O'Connor-McCourt M: Cancer systems biology: exploring cancer-associated genes on cellular networks. Cell Mol Life Sci. 2007, 64 (14): 1752-1762. 10.1007\/s00018-007-7054-6.","journal-title":"Cell Mol Life Sci"},{"issue":"1","key":"1134_CR11","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1049\/iet-syb.2010.0052","volume":"6","author":"ZP Liu","year":"2012","unstructured":"Liu ZP, Wang Y, Zhang XS, Chen L: Network-based analysis of complex diseases. IET Syst Biol. 2012, 6 (1): 22-33. 10.1049\/iet-syb.2010.0052.","journal-title":"IET Syst Biol"},{"issue":"2","key":"1134_CR12","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/ng1165","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. Nat Genet. 2003, 34 (2): 166-76. 10.1038\/ng1165.","journal-title":"Nat Genet"},{"issue":"11","key":"1134_CR13","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/nbt890","volume":"21","author":"Z Bar-Joseph","year":"2003","unstructured":"Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK: Computational discovery of gene modules and regulatory networks. Nat Biotechnol. 2003, 21 (11): 1337-42. 10.1038\/nbt890.","journal-title":"Nat Biotechnol"},{"issue":"4","key":"1134_CR14","first-page":"408","volume":"10","author":"WP Lee","year":"2009","unstructured":"Lee WP, Tzou WS: Computational methods for discovering gene networks from expression data. Brief Bioinform. 2009, 10 (4): 408-423.","journal-title":"Brief Bioinform"},{"key":"1134_CR15","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1007\/978-3-540-78709-9_5","volume-title":"RNA technologies in cardiovascular medicine and research","author":"E Wang","year":"2008","unstructured":"Wang E: RNA technologies in cardiovascular medicine and research. Edited by: Erdmann VA, Poller W, Barciszewski J. 2008, Germany: Springer, 69-86."},{"issue":"1","key":"1134_CR16","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1758-907X-1-6","volume":"1","author":"S Bandyopadhyay","year":"2010","unstructured":"Bandyopadhyay S, Mitra R, Maulik U, Zhang MQ: Development of the human cancer microRNA network. Silence. 2010, 1 (1): 6-10.1186\/1758-907X-1-6.","journal-title":"Silence"},{"key":"1134_CR17","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1101\/gr.098046.109","volume":"20","author":"S Volinia","year":"2010","unstructured":"Volinia S, Galasso M, Costinean S, Tagliavini L, Gamberoni G, Drusco A, Marchesini J, Mascellani N, Sana ME, Jarour RA, Desponts C, Teitell M, Baffa R, Aqeilan R, Iorio V, Taccioli C, Garzon R, Leva GD, Fabbri M, Catozzi M, Previati M, Ambs S, Palumbo T, Garofalo M, Veronese A, Bottoni A, Gasparini P, Harris C, Visone R, Pekarsky P, Chapelle A, Bloomston M, Dillhoff M, Rassenti LZ, Kipps TJ, Huebner K, Pichiorri F, Lenze D, Cairo S, Buendia M, Pineau P, Dejean A, Zanesi N, Rossi S, Calin GA, Liu C, Palatini J, Negrini M, Vecchione A, Rosenberg A, Croce CM: Reprogramming of miRNA networks in cancer and leukemia. Genome Res. 2010, 20: 589-599. 10.1101\/gr.098046.109.","journal-title":"Genome Res"},{"key":"1134_CR18","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/1756-0381-4-17","volume":"4","author":"J Satoh","year":"2011","unstructured":"Satoh J, Tabunoki H: Comprehensive analysis of human microRNA target networks. BioData Mining. 2011, 4: 17-10.1186\/1756-0381-4-17.","journal-title":"BioData Mining"},{"key":"1134_CR19","volume-title":"Brief Bioinform","author":"B Liu","year":"2012","unstructured":"Liu B, Li J, Cairns MJ: Identifying miRNAs, targets and functions. Brief Bioinform. 2012, 10.1093\/bib\/bbs075."},{"key":"1134_CR20","volume-title":"Brief Bioinform","author":"A Muniategui","year":"2012","unstructured":"Muniategui A, Pey J, Planes FJ, Rubio A: Joint analysis of miRNA and mRNA expression data. Brief Bioinform. 2012, doi:10.1093\/bib\/bbs028."},{"issue":"Suppl. 2","key":"1134_CR21","doi-asserted-by":"crossref","first-page":"ii93","DOI":"10.1093\/bioinformatics\/bti1116","volume":"21","author":"S Yoon","year":"2005","unstructured":"Yoon S, De Micheli G: Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics. 2005, 21 (Suppl. 2): ii93-100.","journal-title":"Bioinformatics"},{"key":"1134_CR22","first-page":"114","volume-title":"Detecting microRNA targets by linking sequence, microRNA and gene expression data","author":"J Huang","year":"2006","unstructured":"Huang J, Morris Q, Frey B: Research in Computational Molecular Biology. Detecting microRNA targets by linking sequence, microRNA and gene expression data. 2006, 114-129."},{"issue":"9","key":"1134_CR23","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1093\/bioinformatics\/btm045","volume":"23","author":"JG Joung","year":"2007","unstructured":"Joung JG, Hwang KB, Nam JW, Kim SJ, Zhang BT: Discovery of microRNA-mRNA modules via population-based probabilistic learning. Bioinformatics. 2007, 23 (9): 1141-1147. 10.1093\/bioinformatics\/btm045.","journal-title":"Bioinformatics"},{"issue":"3","key":"1134_CR24","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1093\/bioinformatics\/btn626","volume":"25","author":"JG Joung","year":"2009","unstructured":"Joung JG, Fei Z: Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model. Bioinformatics. 2009, 25 (3): 387-393. 10.1093\/bioinformatics\/btn626.","journal-title":"Bioinformatics"},{"issue":"1","key":"1134_CR25","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1186\/1471-2105-10-408","volume":"10","author":"B Liu","year":"2009","unstructured":"Liu B, Li J, Tsykin A, Liu L, Gaur AB, Goodall GJ: Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy. BMC Bioinformatics. 2009, 10 (1): 408-10.1186\/1471-2105-10-408.","journal-title":"BMC Bioinformatics"},{"issue":"18","key":"1134_CR26","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1093\/bioinformatics\/btq395","volume":"26","author":"E Bonnet","year":"2010","unstructured":"Bonnet E, Michoel T, Van de Peer Y: Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics. 2010, 26 (18): 638-644. 10.1093\/bioinformatics\/btq395.","journal-title":"Bioinformatics"},{"issue":"4","key":"1134_CR27","doi-asserted-by":"publisher","first-page":"e10162","DOI":"10.1371\/journal.pone.0010162","volume":"5","author":"E Bonnet","year":"2010","unstructured":"Bonnet E, Tatari M, Joshi A, Michoel T, Marchal K, Berx G, Van de Peer Y: Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLoS One. 2010, 5 (4): e10162-10.1371\/journal.pone.0010162.","journal-title":"PLoS One"},{"issue":"24","key":"1134_CR28","doi-asserted-by":"publisher","first-page":"3105","DOI":"10.1093\/bioinformatics\/btq576","volume":"26","author":"B Liu","year":"2010","unstructured":"Liu B, Liu L, Tsykin A, Goodall GJ, Green JE, Zhu M, Kim CH, Li J: Identifying functional miRNA-mRNA regulatory modules with correspondence latent Dirichlet allocation. Bioinformatics. 2010, 26 (24): 3105-3111. 10.1093\/bioinformatics\/btq576.","journal-title":"Bioinformatics"},{"issue":"Suppl. 12","key":"1134_CR29","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-9-S12-S5","volume":"9","author":"D Tran","year":"2008","unstructured":"Tran D, Satou K, Ho T: Finding microRNA regulatory modules in human genome using rule induction. BMC Bioinformatics. 2008, 9 (Suppl. 12): S5-","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"1134_CR30","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/j.jbi.2009.01.005","volume":"42","author":"B Liu","year":"2009","unstructured":"Liu B, Li J, Tsykin A: Discovery of functional miRNA-mRNA regulatory modules with computational methods. J Biomed Inform. 2009, 42 (4): 685-691. 10.1016\/j.jbi.2009.01.005.","journal-title":"J Biomed Inform"},{"issue":"13","key":"1134_CR31","doi-asserted-by":"publisher","first-page":"i401","DOI":"10.1093\/bioinformatics\/btr206","volume":"27","author":"S Zhang","year":"2011","unstructured":"Zhang S, Li Q, Liu J, Zhou XJ: A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics. 2011, 27 (13): i401-409. 10.1093\/bioinformatics\/btr206.","journal-title":"Bioinformatics"},{"issue":"1","key":"1134_CR32","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1186\/1471-2164-10-373","volume":"10","author":"X Peng","year":"2009","unstructured":"Peng X, Li Y, Walters KA, Rosenzweig ER, Lederer SL, Aicher LD, Proll S, Katze MG: Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. BMC Genomics. 2009, 10 (1): 373-10.1186\/1471-2164-10-373.","journal-title":"BMC Genomics"},{"issue":"2","key":"1134_CR33","doi-asserted-by":"publisher","first-page":"e8898","DOI":"10.1371\/journal.pone.0008898","volume":"5","author":"J Nunez-Iglesias","year":"2010","unstructured":"Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ: Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer\u2019s disease cortex reveals altered miRNA regulation. PLoS One. 2010, 5 (2): e8898-10.1371\/journal.pone.0008898.","journal-title":"PLoS One"},{"issue":"17","key":"1134_CR34","doi-asserted-by":"publisher","first-page":"2406","DOI":"10.1093\/bioinformatics\/btr410","volume":"27","author":"Y Lu","year":"2011","unstructured":"Lu Y, Zhou Y, Qu W, Deng M, Zhang C: A Lasso regression model for the construction of microRNA-target regulatory networks. Bioinformatics. 2011, 27 (17): 2406-2413. 10.1093\/bioinformatics\/btr410.","journal-title":"Bioinformatics"},{"issue":"6","key":"1134_CR35","doi-asserted-by":"publisher","first-page":"e40130","DOI":"10.1371\/journal.pone.0040130","volume":"7","author":"W Zhang","year":"2012","unstructured":"Zhang W, Edwards A, Fan W, Flemington EK, Zhang K: MiRNA-mRNA correlation-network modules human prostate cancer and the differences between primary and metastatic tumor subtypes. PLoS One. 2012, 7 (6): e40130-10.1371\/journal.pone.0040130.","journal-title":"PLoS One"},{"key":"1134_CR36","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.ccr.2010.05.026","volume":"18","author":"BS Taylor","year":"2010","unstructured":"Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL: Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010, 18: 11-22. 10.1016\/j.ccr.2010.05.026.","journal-title":"Cancer Cell"},{"issue":"1","key":"1134_CR37","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1145\/1656274.1656278","volume":"11","author":"M Hall","year":"2009","unstructured":"Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH: The WEKA data mining software: an update. SIGKDD Explor. 2009, 11 (1): 10-18. 10.1145\/1656274.1656278.","journal-title":"SIGKDD Explor"},{"issue":"3","key":"1134_CR38","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","volume":"27","author":"ME Smoot","year":"2011","unstructured":"Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011, 27 (3): 431-432. 10.1093\/bioinformatics\/btq675.","journal-title":"Bioinformatics"},{"key":"1134_CR39","doi-asserted-by":"publisher","first-page":"D98","DOI":"10.1093\/nar\/gkn714","volume":"37","author":"Q Jiang","year":"2009","unstructured":"Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y: miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009, 37: D98-104. 10.1093\/nar\/gkn714.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1134_CR40","doi-asserted-by":"publisher","first-page":"D721","DOI":"10.1093\/nar\/gkl811","volume":"35","author":"ME Higgins","year":"2007","unstructured":"Higgins ME, Claremont M, Major JE, Sander C, Lash AE: CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res. 2007, 35 (Database issue): D721-D726.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1134_CR41","doi-asserted-by":"publisher","first-page":"D144","DOI":"10.1093\/nar\/gkr965","volume":"40","author":"HM Zhang","year":"2012","unstructured":"Zhang HM, Chen H, Liu W, Liu H, Gong J, Wang H, Guo AY: AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res. 2012, 40 (Database issue): D144-D149.","journal-title":"Nucleic Acids Res"},{"key":"1134_CR42","first-page":"391","volume-title":"Oncogene and Cancer - From Bench to Clinic","author":"T Triulzi","year":"2013","unstructured":"Triulzi T, Iorio MV, Tagliabue E, Casalini P: MicroRNA: new players in metastatic process. Oncogene and Cancer - From Bench to Clinic. Edited by: Siregar Y. 2013, InTech, 391-414."},{"issue":"1","key":"1134_CR43","doi-asserted-by":"publisher","first-page":"4","DOI":"10.4103\/1477-3163.93001","volume":"11","author":"S Dasgupta","year":"2012","unstructured":"Dasgupta S, Srinidhi S, Vishwanatha JK: Oncogenic activation in prostate cancer progression and metastasis: molecular insights and future challenges. J Carcinog. 2012, 11 (1): 4-10.4103\/1477-3163.93001.","journal-title":"J Carcinog"},{"key":"1134_CR44","doi-asserted-by":"publisher","first-page":"R90","DOI":"10.1186\/gb-2010-11-8-r90","volume":"11","author":"D Betel","year":"2010","unstructured":"Betel D, Koppal A, Agius P, Sander C, Leslie C: mirSVR predicted target site scoring method: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 2010, 11: R90-10.1186\/gb-2010-11-8-r90.","journal-title":"Genome Biol"},{"key":"1134_CR45","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nrc1840","volume":"6","author":"A Esquela-Kerscher","year":"2006","unstructured":"Esquela-Kerscher A, Slack FJ: Oncomirs: microRNAs with a role in cancer. Nat Rev Cancer. 2006, 6: 259-269.","journal-title":"Nat Rev Cancer"},{"issue":"2","key":"1134_CR46","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/bjc.2011.462","volume":"106","author":"S Kojima","year":"2012","unstructured":"Kojima S, Chiyomaru T, Kawakami K, Yoshino H, Enokida H, Nohata N, Fuse M, Ichikawa T, Naya Y, Nakagawa M, Seki N: Tumour suppressors miR-1 and miR-133a target the oncogenic function of purine nucleoside phosphorylase (PNP) in prostate cancer. Br J Cancer. 2012, 106 (2): 405-413. 10.1038\/bjc.2011.462.","journal-title":"Br J Cancer"},{"issue":"5","key":"1134_CR47","doi-asserted-by":"publisher","first-page":"e20341","DOI":"10.1371\/journal.pone.0020341","volume":"6","author":"X Peng","year":"2011","unstructured":"Peng X, Guo W, Liu T, Wang X, Tu X, Xiong D, Chen S, Lai Y, Du H, Chen G, Liu G, Tang Y, Huang S, Zou X: Identification of miRs-143 and \u2212145 that is associated with bone metastasis of prostate cancer and involved in the regulation of EMT. PLoS One. 2011, 6 (5): e20341-10.1371\/journal.pone.0020341.","journal-title":"PLoS One"},{"issue":"32","key":"1134_CR48","doi-asserted-by":"publisher","first-page":"23716","DOI":"10.1074\/jbc.M701805200","volume":"282","author":"S Galardi","year":"2007","unstructured":"Galardi S, Mercatelli N, Giorda E, Massalini S, Frajese GV, Ciafr\u00e8 SA, Farace MG: miR-221 and miR-222 expression affects the proliferation potential of human prostate carcinoma cell lines by targeting p27Kip1. J Biol Chem. 2007, 282 (32): 23716-23724. 10.1074\/jbc.M701805200.","journal-title":"J Biol Chem"},{"issue":"1","key":"1134_CR49","doi-asserted-by":"publisher","first-page":"e8697","DOI":"10.1371\/journal.pone.0008697","volume":"5","author":"L Vrba","year":"2010","unstructured":"Vrba L, Jensen TJ, Garbe JC, Heimark RL, Cress AE, Dickinson S, Stampfer MR, Futscher BW: Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells. PLoS One. 2010, 5 (1): e8697-10.1371\/journal.pone.0008697.","journal-title":"PLoS One"},{"issue":"2","key":"1134_CR50","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1158\/0008-5472.CAN-08-3415","volume":"69","author":"CD Scharer","year":"2009","unstructured":"Scharer CD, McCabe CD, Ali-Seyed M, Berger MF, Bulyk ML, Moreno CS: Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells. Cancer Res. 2009, 69 (2): 709-717. 10.1158\/0008-5472.CAN-08-3415.","journal-title":"Cancer Res"},{"issue":"6","key":"1134_CR51","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.2353\/ajpath.2008.071054","volume":"172","author":"J Abdulghani","year":"2008","unstructured":"Abdulghani J, Gu L, Dagvadorj A, Lutz J, Leiby B, Bonuccelli G, Lisanti MP, Zellweger T, Alanen K, Mirtti T, Visakorpi T, Bubendorf L, Nevalainen MT: STAT3 promotes metastatic progression of prostate cancer. Am J Pathol. 2008, 172 (6): 1717-1728. 10.2353\/ajpath.2008.071054.","journal-title":"Am J Pathol"},{"issue":"2","key":"1134_CR52","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1677\/ERC-09-0328","volume":"17","author":"L Gu","year":"2010","unstructured":"Gu L, Vogiatzi P, Puhr M, Dagvadorj A, Lutz J, Ryder A, Addya S, Fortina P, Cooper C, Leiby B, Dasgupta A, Hyslop T, Bubendorf L, Alanen K, Mirtti T, Nevalainen MT: STAT5 promotes metastatic behavior of human prostate cancer cells in vitro and in vivo. Endocr Relat Cancer. 2010, 17 (2): 481-493. 10.1677\/ERC-09-0328.","journal-title":"Endocr Relat Cancer"},{"issue":"3","key":"1134_CR53","doi-asserted-by":"publisher","first-page":"143","DOI":"10.4161\/jkst.19573","volume":"1","author":"A Haghikia","year":"2012","unstructured":"Haghikia A, Hoch M, Stapel B, Hilfiker-Kleiner D: STAT3 regulation of and by microRNAs in development and disease. JAK STAT. 2012, 1 (3): 143-105. 10.4161\/jkst.19573.","journal-title":"JAK STAT"},{"issue":"4","key":"1134_CR54","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1177\/1947601910371978","volume":"1","author":"R Steele","year":"2010","unstructured":"Steele R, Mott JL, Ray RB: MBP-1 upregulates miR-29b that represses Mcl-1, collagens, and matrix-metalloproteinase-2 in prostate cancer cells. Genes Cancer. 2010, 1 (4): 381-387. 10.1177\/1947601910371978.","journal-title":"Genes Cancer"},{"issue":"12","key":"1134_CR55","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","volume":"27","author":"A Liberzon","year":"2011","unstructured":"Liberzon A, Subramanian A, Pinchback R, Thorvaldsd\u00f3ttir H, Tamayo P, Mesirov JP: Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011, 27 (12): 1739-1740. 10.1093\/bioinformatics\/btr260.","journal-title":"Bioinformatics"},{"key":"1134_CR56","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1038\/nrurol.2012.116","volume":"9","author":"RM Kypta","year":"2012","unstructured":"Kypta RM, Waxman J: Wnt\/\u03b2-catenin signalling in prostate cancer. Nat Rev Urol. 2012, 9: 418-428. 10.1038\/nrurol.2012.116.","journal-title":"Nat Rev Urol"},{"issue":"2","key":"1134_CR57","first-page":"367","volume":"14","author":"S Schwartz Jr","year":"1999","unstructured":"Schwartz S, Caceres C, Morote J, De Torres I, Rodriguez-Vallejo JM, Gonzalez J, Reventos J: Gains of the relative genomic content of ErbB1 and ErbB2 in prostate carcinoma and their association with metastasis. Int J Oncol. 1999, 14 (2): 367-371.","journal-title":"Int J Oncol"},{"issue":"13","key":"1134_CR58","doi-asserted-by":"publisher","first-page":"4329","DOI":"10.1158\/0008-5472.CAN-11-0640","volume":"71","author":"P Raychaudhuri","year":"2011","unstructured":"Raychaudhuri P, Park HJ: FoxM1: a master regulator of tumor metastasis. Cancer Res. 2011, 71 (13): 4329-4333. 10.1158\/0008-5472.CAN-11-0640.","journal-title":"Cancer Res"},{"issue":"6","key":"1134_CR59","doi-asserted-by":"publisher","first-page":"2034","DOI":"10.1158\/0008-5472.CAN-10-3776","volume":"71","author":"A Wolfer","year":"2011","unstructured":"Wolfer A, Ramaswamy S: MYC and metastasis. Cancer Res. 2011, 71 (6): 2034-2037. 10.1158\/0008-5472.CAN-10-3776.","journal-title":"Cancer Res"},{"issue":"5659","key":"1134_CR60","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1094068","volume":"303","author":"N Friedman","year":"2004","unstructured":"Friedman N: Inferring cellular networks using probabilistic graphical models. Science. 2004, 303 (5659): 799-805. 10.1126\/science.1094068.","journal-title":"Science"},{"issue":"1","key":"1134_CR61","doi-asserted-by":"publisher","first-page":"R22","DOI":"10.1186\/gb-2008-9-1-r22","volume":"9","author":"A Ivan","year":"2008","unstructured":"Ivan A, Halfon M, Sinha S: Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol. 2008, 9 (1): R22-10.1186\/gb-2008-9-1-r22.","journal-title":"Genome Biol"},{"issue":"3","key":"1134_CR62","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1109\/MCI.2008.926615","volume":"3","author":"BT Zhang","year":"2008","unstructured":"Zhang BT: Hypernetworks: A molecular evolutionary architecture for cognitive learning and memory. IEEE Computational Intelligence Magazine. 2008, 3 (3): 49-63.","journal-title":"IEEE Computational Intelligence Magazine"},{"key":"1134_CR63","first-page":"2299","volume-title":"Evolutionary layered hypernetworks for identifying microRNA-mRNA regulatory modules","author":"SJ Kim","year":"2010","unstructured":"Kim SJ, Ha JW, Zhang BT: Proceedings of IEEE World Congress Computational Intelligence. Evolutionary layered hypernetworks for identifying microRNA-mRNA regulatory modules. 2010, (WCCI-CEC 2010, 2299-2306."},{"key":"1134_CR64","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511543241","volume-title":"Radial basis functions: theory and implementations","author":"MD Buhmann","year":"2003","unstructured":"Buhmann MD: Cambridge Monographs on Applied and Computational Mathematics (Vol.12). Radial basis functions: theory and implementations. 2003, Cambridge University Press"},{"issue":"6","key":"1134_CR65","doi-asserted-by":"publisher","first-page":"066138","DOI":"10.1103\/PhysRevE.69.066138","volume":"69","author":"A Kraskov","year":"2004","unstructured":"Kraskov A, St\u00f6gbauer H, Grassberger P: Estimating mutual information. Phys Rev E. 2004, 69 (6): 066138-","journal-title":"Phys Rev E"},{"issue":"suppl 1","key":"1134_CR66","doi-asserted-by":"publisher","first-page":"i213","DOI":"10.1093\/bioinformatics\/bti1049","volume":"21","author":"H Hu","year":"2005","unstructured":"Hu H, Yan X, Huang Y, Han J, Zhou XJ: Mining coherent dense subgraphs across massive biological networks for functional discovery. Bioinformatics. 2005, 21 (suppl 1): i213-i221. 10.1093\/bioinformatics\/bti1049.","journal-title":"Bioinformatics"},{"issue":"2","key":"1134_CR67","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1049\/iet-syb:20060038","volume":"1","author":"O Mason","year":"2007","unstructured":"Mason O, Verwoerd M: Graph theory and networks in biology. IET Syst Biol. 2007, 1 (2): 89-119. 10.1049\/iet-syb:20060038.","journal-title":"IET Syst Biol"},{"issue":"13","key":"1134_CR68","doi-asserted-by":"publisher","first-page":"i577","DOI":"10.1093\/bioinformatics\/btm227","volume":"23","author":"X Yan","year":"2007","unstructured":"Yan X, Mehan MR, Huang Y, Waterman MS, Yu PS, Zhou XZ: A graph-based approach to systematically reconstruct human transcriptional regulatory modules. Bioinformatics. 2007, 23 (13): i577-i586. 10.1093\/bioinformatics\/btm227.","journal-title":"Bioinformatics"},{"key":"1134_CR69","first-page":"556","volume-title":"A hyper-graph approach for analyzing transcriptional networks in breast cance","author":"E Ramadan","year":"2010","unstructured":"Ramadan E, Perincheri P, Tuck D: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology. A hyper-graph approach for analyzing transcriptional networks in breast cance. 2010, 556-562."}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-7-47.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,12]],"date-time":"2024-05-12T16:41:06Z","timestamp":1715532066000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-7-47"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6,19]]},"references-count":69,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["1134"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-7-47","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,6,19]]},"assertion":[{"value":"1 November 2012","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 June 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 June 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"47"}}