{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:46:28Z","timestamp":1767962788412,"version":"3.49.0"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/1752-0509-9-s1-s5","type":"journal-article","created":{"date-parts":[[2015,6,18]],"date-time":"2015-06-18T16:39:43Z","timestamp":1434645583000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks"],"prefix":"10.1186","volume":"9","author":[{"given":"Wen-Tsong","family":"Hsieh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke-Rung","family":"Tzeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin-Shuei","family":"Ciou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey JP","family":"Tsai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nilubon","family":"Kurubanjerdjit","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chien-Hung","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ka-Lok","family":"Ng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,1,21]]},"reference":[{"key":"1420_CR1","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1093\/oxfordjournals.molbev.a003913","volume":"18","author":"A Wagner","year":"2001","unstructured":"Wagner A: The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular biology and evolution. 2001, 18: 1283-1292. 10.1093\/oxfordjournals.molbev.a003913.","journal-title":"Molecular biology and evolution"},{"key":"1420_CR2","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/35036627","volume":"407","author":"H Jeong","year":"2000","unstructured":"Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL: The large-scale organization of metabolic networks. Nature. 2000, 407: 651-654. 10.1038\/35036627.","journal-title":"Nature"},{"key":"1420_CR3","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1093\/bioinformatics\/19.2.270","volume":"19","author":"H Ma","year":"2003","unstructured":"Ma H, Zeng AP: Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics. 2003, 19: 270-277. 10.1093\/bioinformatics\/19.2.270.","journal-title":"Bioinformatics"},{"key":"1420_CR4","doi-asserted-by":"publisher","DOI":"10.1002\/9780470020036","volume-title":"Bioinformatics: genomics and post-genomics","author":"F Dardel","year":"2006","unstructured":"Dardel F, K\u00e9p\u00e8s F: Bioinformatics: genomics and post-genomics. 2006, Chichester, England; Hoboken, NJ: John Wiley & Sons"},{"key":"1420_CR5","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":"1420_CR6","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1752-0509-3-10","volume":"3","author":"A Ma'ayan","year":"2009","unstructured":"Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R: SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC systems biology. 2009, 3: 10-10.1186\/1752-0509-3-10.","journal-title":"BMC systems biology"},{"key":"1420_CR7","doi-asserted-by":"publisher","first-page":"4649","DOI":"10.1073\/pnas.97.9.4649","volume":"97","author":"TM Yi","year":"2000","unstructured":"Yi TM, Huang Y, Simon MI, Doyle J: Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proceedings of the National Academy of Sciences of the United States of America. 2000, 97: 4649-4653. 10.1073\/pnas.97.9.4649.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"1420_CR8","doi-asserted-by":"publisher","first-page":"11980","DOI":"10.1073\/pnas.2133841100","volume":"100","author":"S Mangan","year":"2003","unstructured":"Mangan S, Alon U: Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Sciences of the United States of America. 2003, 100: 11980-11985. 10.1073\/pnas.2133841100.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"1420_CR9","doi-asserted-by":"publisher","first-page":"2005 0006","DOI":"10.1038\/msb4100010","volume":"1","author":"S Kalir","year":"2005","unstructured":"Kalir S, Mangan S, Alon U: A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Molecular systems biology. 2005, 1: 2005 0006-","journal-title":"Molecular systems biology"},{"key":"1420_CR10","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1038\/ng881","volume":"31","author":"SS Shen-Orr","year":"2002","unstructured":"Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional regulation network of Escherichia coli. Nature genetics. 2002, 31: 64-68. 10.1038\/ng881.","journal-title":"Nature genetics"},{"key":"1420_CR11","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1016\/j.jmb.2005.12.003","volume":"356","author":"S Mangan","year":"2006","unstructured":"Mangan S, Itzkovitz S, Zaslaver A, Alon U: The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. Journal of molecular biology. 2006, 356: 1073-1081. 10.1016\/j.jmb.2005.12.003.","journal-title":"Journal of molecular biology"},{"key":"1420_CR12","doi-asserted-by":"publisher","first-page":"e328","DOI":"10.1371\/journal.pbio.0020328","volume":"2","author":"P Eichenberger","year":"2004","unstructured":"Eichenberger P, Fujita M, Jensen ST, Conlon EM, Rudner DZ, Wang ST, Ferguson C, Haga K, Sato T, Liu JS, Losick R: The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS biology. 2004, 2: e328-10.1371\/journal.pbio.0020328.","journal-title":"PLoS biology"},{"key":"1420_CR13","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1126\/science.298.5594.824","volume":"298","author":"R Milo","year":"2002","unstructured":"Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks. Science. 2002, 298: 824-827. 10.1126\/science.298.5594.824.","journal-title":"Science"},{"key":"1420_CR14","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1075090","volume":"298","author":"TI Lee","year":"2002","unstructured":"Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002, 298: 799-804. 10.1126\/science.1075090.","journal-title":"Science"},{"key":"1420_CR15","doi-asserted-by":"publisher","first-page":"1378","DOI":"10.1126\/science.1089769","volume":"303","author":"DT Odom","year":"2004","unstructured":"Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, et al: Control of pancreas and liver gene expression by HNF transcription factors. Science. 2004, 303: 1378-1381. 10.1126\/science.1089769.","journal-title":"Science"},{"key":"1420_CR16","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1016\/j.cell.2005.08.020","volume":"122","author":"LA Boyer","year":"2005","unstructured":"Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, et al: Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005, 122: 947-956. 10.1016\/j.cell.2005.08.020.","journal-title":"Cell"},{"key":"1420_CR17","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1016\/j.ydbio.2005.11.035","volume":"290","author":"N Iranfar","year":"2006","unstructured":"Iranfar N, Fuller D, Loomis WF: Transcriptional regulation of post-aggregation genes in Dictyostelium by a feed-forward loop involving GBF and LagC. Developmental biology. 2006, 290: 460-469. 10.1016\/j.ydbio.2005.11.035.","journal-title":"Developmental biology"},{"key":"1420_CR18","doi-asserted-by":"publisher","first-page":"1538","DOI":"10.1126\/science.1089167","volume":"303","author":"R Milo","year":"2004","unstructured":"Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U: Superfamilies of evolved and designed networks. Science. 2004, 303: 1538-1542. 10.1126\/science.1089167.","journal-title":"Science"},{"key":"1420_CR19","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":"1420_CR20","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1126\/science.1108876","volume":"309","author":"A Ma'ayan","year":"2005","unstructured":"Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, et al: Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science. 2005, 309: 1078-1083. 10.1126\/science.1108876.","journal-title":"Science"},{"key":"1420_CR21","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/1471-2164-7-108","volume":"7","author":"PJ Ingram","year":"2006","unstructured":"Ingram PJ, Stumpf MP, Stark J: Network motifs: structure does not determine function. BMC genomics. 2006, 7: 108-10.1186\/1471-2164-7-108.","journal-title":"BMC genomics"},{"key":"1420_CR22","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/j.sbi.2004.05.004","volume":"14","author":"MM Babu","year":"2004","unstructured":"Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA: Structure and evolution of transcriptional regulatory networks. Current opinion in structural biology. 2004, 14: 283-291. 10.1016\/j.sbi.2004.05.004.","journal-title":"Current opinion in structural biology"},{"key":"1420_CR23","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.ydbio.2006.02.051","volume":"294","author":"G Swiers","year":"2006","unstructured":"Swiers G, Patient R, Loose M: Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification. Developmental biology. 2006, 294: 525-540. 10.1016\/j.ydbio.2006.02.051.","journal-title":"Developmental biology"},{"key":"1420_CR24","first-page":"278","volume-title":"3rd International Conference on Bioscience and Bioinformatics, Switzerland","author":"H Chien-Hung","year":"2012","unstructured":"Chien-Hung H, Ke-Rung T, Ka-lok N: In silico study of cancer network motifs. 3rd International Conference on Bioscience and Bioinformatics, Switzerland. 2012, 278-283."},{"key":"1420_CR25","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1529\/biophysj.107.105106","volume":"94","author":"JR Kim","year":"2008","unstructured":"Kim JR, Yoon Y, Cho KH: Coupled feedback loops form dynamic motifs of cellular networks. Biophysical journal. 2008, 94: 359-365. 10.1529\/biophysj.107.105106.","journal-title":"Biophysical journal"},{"key":"1420_CR26","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1126\/science.1156951","volume":"321","author":"TY Tsai","year":"2008","unstructured":"Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, Ferrell JE: Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science. 2008, 321: 126-129. 10.1126\/science.1156951.","journal-title":"Science"},{"key":"1420_CR27","volume-title":"The biology of cancer","author":"RA Weinberg","year":"2007","unstructured":"Weinberg RA: The biology of cancer. 2007, New York: Garland Science"},{"key":"1420_CR28","doi-asserted-by":"crossref","first-page":"3368","DOI":"10.1038\/srep03368","volume":"3","author":"L Chen","year":"2013","unstructured":"Chen L, Qu X, Cao M, Zhou Y, Li W, Liang B, Li W, He W, Feng C, Jia X, He Y: Identification of breast cancer patients based on human signaling network motifs. Scientific reports. 2013, 3: 3368-","journal-title":"Scientific reports"},{"key":"1420_CR29","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","volume":"116","author":"DP Bartel","year":"2004","unstructured":"Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004, 116: 281-297. 10.1016\/S0092-8674(04)00045-5.","journal-title":"Cell"},{"key":"1420_CR30","doi-asserted-by":"publisher","first-page":"2364","DOI":"10.1038\/ncomms3364","volume":"4","author":"V Siciliano","year":"2013","unstructured":"Siciliano V, Garzilli I, Fracassi C, Criscuolo S, Ventre S, di Bernardo D: MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise. Nature communications. 2013, 4: 2364-","journal-title":"Nature communications"},{"key":"1420_CR31","doi-asserted-by":"publisher","first-page":"025107","DOI":"10.1063\/1.4808248","volume":"23","author":"C Kadelka","year":"2013","unstructured":"Kadelka C, Murrugarra D, Laubenbacher R: Stabilizing gene regulatory networks through feedforward loops. Chaos. 2013, 23: 025107-10.1063\/1.4808248.","journal-title":"Chaos"},{"key":"1420_CR32","doi-asserted-by":"publisher","first-page":"2477","DOI":"10.4161\/cc.8.16.9271","volume":"8","author":"EE Cohen","year":"2009","unstructured":"Cohen EE, Rosner MR: MicroRNA-regulated feed forward loop network. Cell cycle. 2009, 8: 2477-2478. 10.4161\/cc.8.16.9271.","journal-title":"Cell cycle"},{"key":"1420_CR33","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1038\/msb4100089","volume":"2","author":"Q Cui","year":"2006","unstructured":"Cui Q, Yu Z, Purisima EO, Wang E: Principles of microRNA regulation of a human cellular signaling network. Molecular systems biology. 2006, 2: 46-","journal-title":"Molecular systems biology"},{"key":"1420_CR34","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1038\/nature03552","volume":"435","author":"L He","year":"2005","unstructured":"He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM: A microRNA polycistron as a potential human oncogene. Nature. 2005, 435: 828-833. 10.1038\/nature03552.","journal-title":"Nature"},{"key":"1420_CR35","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. Nature reviews Cancer. 2006, 6: 259-269. 10.1038\/nrc1840.","journal-title":"Nature reviews Cancer"},{"key":"1420_CR36","first-page":"157","volume-title":"Recent Advances in Computer Science","author":"T Ke-Rung","year":"2013","unstructured":"Ke-Rung T, Jin-Shuei C, Chien-Hung H, Ka-lok N: Identification of microRNA-regulated network motifs for cancer disease pathways. Recent Advances in Computer Science. 2013, 157-164."},{"key":"1420_CR37","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gks1239","volume":"41","author":"A Nakaya","year":"2013","unstructured":"Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, et al: KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic acids research. 2013, 41: D353-357. 10.1093\/nar\/gks1239.","journal-title":"Nucleic acids research"},{"key":"1420_CR38","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1186\/1471-2105-11-435","volume":"11","author":"O Friard","year":"2010","unstructured":"Friard O, Re A, Taverna D, De Bortoli M, Cora D: CircuitsDB: a database of mixed microRNA\/transcription factor feed-forward regulatory circuits in human and mouse. BMC bioinformatics. 2010, 11: 435-10.1186\/1471-2105-11-435.","journal-title":"BMC bioinformatics"},{"key":"1420_CR39","doi-asserted-by":"publisher","first-page":"1360","DOI":"10.1039\/c3mb25518b","volume":"9","author":"D Sengupta","year":"2013","unstructured":"Sengupta D, Bandyopadhyay S: Topological patterns in microRNA-gene regulatory network: studies in colorectal and breast cancer. Molecular bioSystems. 2013, 9: 1360-1371. 10.1039\/c3mb25518b.","journal-title":"Molecular bioSystems"},{"key":"1420_CR40","doi-asserted-by":"publisher","first-page":"1025","DOI":"10.1111\/j.1365-2443.2005.00897.x","volume":"10","author":"S Ishihara","year":"2005","unstructured":"Ishihara S, Fujimoto K, Shibata T: Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes to cells: devoted to molecular & cellular mechanisms. 2005, 10: 1025-1038. 10.1111\/j.1365-2443.2005.00897.x.","journal-title":"Genes to cells: devoted to molecular & cellular mechanisms"},{"key":"1420_CR41","doi-asserted-by":"publisher","first-page":"3572","DOI":"10.1093\/bioinformatics\/bti556","volume":"21","author":"F Schreiber","year":"2005","unstructured":"Schreiber F, Schwobbermeyer H: MAVisto: a tool for the exploration of network motifs. Bioinformatics. 2005, 21: 3572-3574. 10.1093\/bioinformatics\/bti556.","journal-title":"Bioinformatics"},{"key":"1420_CR42","doi-asserted-by":"publisher","first-page":"1152","DOI":"10.1093\/bioinformatics\/btl038","volume":"22","author":"S Wernicke","year":"2006","unstructured":"Wernicke S, Rasche F: FANMOD: a tool for fast network motif detection. Bioinformatics. 2006, 22: 1152-1153. 10.1093\/bioinformatics\/btl038.","journal-title":"Bioinformatics"},{"key":"1420_CR43","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1093\/bioinformatics\/btm032","volume":"23","author":"A Ferro","year":"2007","unstructured":"Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D: NetMatch: a Cytoscape plugin for searching biological networks. Bioinformatics. 2007, 23: 910-912. 10.1093\/bioinformatics\/btm032.","journal-title":"Bioinformatics"},{"key":"1420_CR44","doi-asserted-by":"publisher","first-page":"5451","DOI":"10.1074\/jbc.R800056200","volume":"284","author":"A Ma'ayan","year":"2009","unstructured":"Ma'ayan A: Insights into the organization of biochemical regulatory networks using graph theory analyses. The Journal of biological chemistry. 2009, 284: 5451-5455. 10.1074\/jbc.R800056200.","journal-title":"The Journal of biological chemistry"},{"key":"1420_CR45","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1049\/iet-syb:20050085","volume":"1","author":"SN Sreenath","year":"2007","unstructured":"Sreenath SN, Soebiyanto R, Mesarovic MD, Wolkenhauer O: Coordination of crosstalk between MAPK-PKC pathways: an exploratory study. IET systems biology. 2007, 1: 33-40. 10.1049\/iet-syb:20050085.","journal-title":"IET systems biology"},{"key":"1420_CR46","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1146\/annurev.arplant.55.031903.141627","volume":"55","author":"JF Harper","year":"2004","unstructured":"Harper JF, Breton G, Harmon A: Decoding Ca(2+) signals through plant protein kinases. Annual review of plant biology. 2004, 55: 263-288. 10.1146\/annurev.arplant.55.031903.141627.","journal-title":"Annual review of plant biology"},{"key":"1420_CR47","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1016\/j.pbi.2007.04.020","volume":"10","author":"T Eulgem","year":"2007","unstructured":"Eulgem T, Somssich IE: Networks of WRKY transcription factors in defense signaling. Current opinion in plant biology. 2007, 10: 366-371. 10.1016\/j.pbi.2007.04.020.","journal-title":"Current opinion in plant biology"},{"key":"1420_CR48","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1042\/BJ20080625","volume":"413","author":"J Colcombet","year":"2008","unstructured":"Colcombet J, Hirt H: Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes. The Biochemical journal. 2008, 413: 217-226. 10.1042\/BJ20080625.","journal-title":"The Biochemical journal"},{"key":"1420_CR49","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/j.tplants.2010.02.006","volume":"15","author":"PJ Rushton","year":"2010","unstructured":"Rushton PJ, Somssich IE, Ringler P, Shen QJ: WRKY transcription factors. Trends in plant science. 2010, 15: 247-258. 10.1016\/j.tplants.2010.02.006.","journal-title":"Trends in plant science"},{"key":"1420_CR50","doi-asserted-by":"publisher","first-page":"355","DOI":"10.4137\/EBO.S12012","volume":"9","author":"K Konganti","year":"2013","unstructured":"Konganti K, Wang G, Yang E, Cai JJ: SBEToolbox: A Matlab Toolbox for Biological Network Analysis. Evolutionary bioinformatics online. 2013, 9: 355-362.","journal-title":"Evolutionary bioinformatics online"},{"key":"1420_CR51","doi-asserted-by":"publisher","first-page":"3816","DOI":"10.1182\/blood-2010-05-285064","volume":"117","author":"K Vargova","year":"2011","unstructured":"Vargova K, Curik N, Burda P, Basova P, Kulvait V, Pospisil V, Savvulidi F, Kokavec J, Necas E, Berkova A, et al: MYB transcriptionally regulates the miR-155 host gene in chronic lymphocytic leukemia. Blood. 2011, 117: 3816-3825. 10.1182\/blood-2010-05-285064.","journal-title":"Blood"},{"key":"1420_CR52","doi-asserted-by":"publisher","first-page":"2806","DOI":"10.1101\/gad.1872909","volume":"23","author":"P Mu","year":"2009","unstructured":"Mu P, Han YC, Betel D, Yao E, Squatrito M, Ogrodowski P, de Stanchina E, D'Andrea A, Sander C, Ventura A: Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes & development. 2009, 23: 2806-2811. 10.1101\/gad.1872909.","journal-title":"Genes & development"},{"key":"1420_CR53","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1093\/bioinformatics\/bts715","volume":"29","author":"JS Chen","year":"2013","unstructured":"Chen JS, Hung WS, Chan HH, Tsai SJ, Sun HS: In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma. Bioinformatics. 2013, 29: 420-427. 10.1093\/bioinformatics\/bts715.","journal-title":"Bioinformatics"},{"key":"1420_CR54","doi-asserted-by":"publisher","DOI":"10.4135\/9781412953979","volume-title":"Encyclopedia of cancer and society","author":"GA Colditz","year":"2007","unstructured":"Colditz GA: Encyclopedia of cancer and society. 2007, Los Angeles: Sage Publications"},{"key":"1420_CR55","unstructured":"private communication."},{"key":"1420_CR56","doi-asserted-by":"publisher","first-page":"D78","DOI":"10.1093\/nar\/gkt1266","volume":"42","author":"SD Hsu","year":"2014","unstructured":"Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, et al: miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic acids research. 2014, 42: D78-85. 10.1093\/nar\/gkt1266.","journal-title":"Nucleic acids research"},{"key":"1420_CR57","doi-asserted-by":"publisher","first-page":"D155","DOI":"10.1093\/nar\/gkn809","volume":"37","author":"GL Papadopoulos","year":"2009","unstructured":"Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG: The database of experimentally supported targets: a functional update of TarBase. Nucleic acids research. 2009, 37: D155-158. 10.1093\/nar\/gkn809.","journal-title":"Nucleic acids research"},{"key":"1420_CR58","doi-asserted-by":"publisher","first-page":"D177","DOI":"10.1093\/nar\/gks1060","volume":"41","author":"JH Yang","year":"2013","unstructured":"Yang JH, Li JH, Jiang S, Zhou H, Qu LH: ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic acids research. 2013, 41: D177-187. 10.1093\/nar\/gks1060.","journal-title":"Nucleic acids research"},{"key":"1420_CR59","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: i401-409. 10.1093\/bioinformatics\/btr206.","journal-title":"Bioinformatics"},{"key":"1420_CR60","doi-asserted-by":"publisher","first-page":"i89","DOI":"10.1093\/bioinformatics\/btt231","volume":"29","author":"HS Le","year":"2013","unstructured":"Le HS, Bar-Joseph Z: Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. Bioinformatics. 2013, 29: i89-97. 10.1093\/bioinformatics\/btt231.","journal-title":"Bioinformatics"},{"key":"1420_CR61","doi-asserted-by":"publisher","first-page":"2627","DOI":"10.1093\/bioinformatics\/btu373","volume":"30","author":"Y Li","year":"2014","unstructured":"Li Y, Liang C, Wong KC, Luo J, Zhang Z: Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. Bioinformatics. 2014, 30: 2627-2635. 10.1093\/bioinformatics\/btu373.","journal-title":"Bioinformatics"},{"key":"1420_CR62","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/j.1460-2075.1995.tb07000.x","volume":"14","author":"T Kinoshita","year":"1995","unstructured":"Kinoshita T, Yokota T, Arai K, Miyajima A: Suppression of apoptotic death in hematopoietic cells by signalling through the IL-3\/GM-CSF receptors. The EMBO journal. 1995, 14: 266-275.","journal-title":"The EMBO journal"},{"key":"1420_CR63","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1016\/j.ctrv.2003.07.007","volume":"30","author":"JA Fresno Vara","year":"2004","unstructured":"Fresno Vara JA, Casado E, de Castro J, Cejas P, Belda-Iniesta C, Gonzalez-Baron M: PI3K\/Akt signalling pathway and cancer. Cancer treatment reviews. 2004, 30: 193-204. 10.1016\/j.ctrv.2003.07.007.","journal-title":"Cancer treatment reviews"},{"key":"1420_CR64","first-page":"11","volume":"24","author":"T Mukohara","year":"2004","unstructured":"Mukohara T, Kudoh S, Matsuura K, Yamauchi S, Kimura T, Yoshimura N, Kanazawa H, Hirata K, Inoue K, Wanibuchi H, et al: Activated Akt expression has significant correlation with EGFR and TGF-alpha expressions in stage I NSCLC. Anticancer research. 2004, 24: 11-17.","journal-title":"Anticancer research"},{"key":"1420_CR65","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1038\/sj.onc.1202422","volume":"18","author":"AM Tari","year":"1999","unstructured":"Tari AM, Hung MC, Li K, Lopez-Berestein G: Growth inhibition of breast cancer cells by Grb2 downregulation is correlated with inactivation of mitogen-activated protein kinase in EGFR, but not in ErbB2, cells. Oncogene. 1999, 18: 1325-1332. 10.1038\/sj.onc.1202422.","journal-title":"Oncogene"},{"key":"1420_CR66","doi-asserted-by":"publisher","first-page":"D530","DOI":"10.1093\/nar\/gks1050","volume":"41","author":"JA Blake","year":"2013","unstructured":"Gene Ontology C, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, et al: Gene Ontology annotations and resources. Nucleic acids research. 2013, 41: D530-535.","journal-title":"Nucleic acids research"},{"key":"1420_CR67","doi-asserted-by":"publisher","first-page":"R83","DOI":"10.1530\/ERC-12-0394","volume":"20","author":"RL Bitting","year":"2013","unstructured":"Bitting RL, Armstrong AJ: Targeting the PI3K\/Akt\/mTOR pathway in castration-resistant prostate cancer. Endocrine-related cancer. 2013, 20: R83-99. 10.1530\/ERC-12-0394.","journal-title":"Endocrine-related cancer"},{"key":"1420_CR68","doi-asserted-by":"publisher","first-page":"378","DOI":"10.4103\/1008-682X.122876","volume":"16","author":"MP Edlind","year":"2014","unstructured":"Edlind MP, Hsieh AC: PI3K-AKT-mTOR signaling in prostate cancer progression and androgen deprivation therapy resistance. Asian journal of andrology. 2014, 16: 378-386. 10.4103\/1008-682X.122876.","journal-title":"Asian journal of andrology"},{"key":"1420_CR69","doi-asserted-by":"publisher","first-page":"237","DOI":"10.2174\/156800909787580999","volume":"9","author":"TM Morgan","year":"2009","unstructured":"Morgan TM, Koreckij TD, Corey E: Targeted therapy for advanced prostate cancer: inhibition of the PI3K\/Akt\/mTOR pathway. Current cancer drug targets. 2009, 9: 237-249. 10.2174\/156800909787580999.","journal-title":"Current cancer drug targets"},{"key":"1420_CR70","first-page":"11","volume":"32","author":"M Kaarbo","year":"2010","unstructured":"Kaarbo M, Mikkelsen OL, Malerod L, Qu S, Lobert VH, Akgul G, Halvorsen T, Maelandsmo GM, Saatcioglu F: PI3K-AKT-mTOR pathway is dominant over androgen receptor signaling in prostate cancer cells. Cellular oncology: the official journal of the International Society for Cellular Oncology. 2010, 32: 11-27.","journal-title":"Cellular oncology: the official journal of the International Society for Cellular Oncology"},{"key":"1420_CR71","doi-asserted-by":"publisher","first-page":"1424","DOI":"10.1002\/ijc.22862","volume":"121","author":"S Shukla","year":"2007","unstructured":"Shukla S, Maclennan GT, Hartman DJ, Fu P, Resnick MI, Gupta S: Activation of PI3K-Akt signaling pathway promotes prostate cancer cell invasion. International journal of cancer Journal international du cancer. 2007, 121: 1424-1432. 10.1002\/ijc.22862.","journal-title":"International journal of cancer Journal international du cancer"},{"key":"1420_CR72","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.ceb.2008.12.010","volume":"21","author":"NE Hynes","year":"2009","unstructured":"Hynes NE, MacDonald G: ErbB receptors and signaling pathways in cancer. Current opinion in cell biology. 2009, 21: 177-184. 10.1016\/j.ceb.2008.12.010.","journal-title":"Current opinion in cell biology"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-9-S1-S5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T08:50:57Z","timestamp":1630572657000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-9-S1-S5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,21]]},"references-count":72,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["1420"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-9-s1-s5","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,1,21]]},"assertion":[{"value":"21 January 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S5"}}