{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T18:33:53Z","timestamp":1721327633790},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,9,7]],"date-time":"2018-09-07T00:00:00Z","timestamp":1536278400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Netw Model Anal Health Inform Bioinforma"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1007\/s13721-018-0175-z","type":"journal-article","created":{"date-parts":[[2018,9,7]],"date-time":"2018-09-07T13:25:14Z","timestamp":1536326714000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Network-based approach to understand dynamic behaviour of Wnt signaling pathway regulatory elements in colorectal cancer"],"prefix":"10.1007","volume":"7","author":[{"given":"Ankita","family":"Shukla","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiratha Raj","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,9,7]]},"reference":[{"key":"175_CR1","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1038\/nrg2102","volume":"8","author":"U Alon","year":"2007","unstructured":"Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8:450\u2013461. \n                    https:\/\/doi.org\/10.1038\/nrg2102","journal-title":"Nat Rev Genet"},{"key":"175_CR2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-310912","author":"M Arnold","year":"2007","unstructured":"Arnold M, Sierra MS, Laversanne M, Soerjomataram I, Jemal A, Bray F (2016) Global patterns and trends in colorectal cancer incidence and mortality. Gut. \n                    https:\/\/doi.org\/10.1136\/gutjnl-2015-310912","journal-title":"Gut"},{"key":"175_CR3","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/nrg2918","volume":"12","author":"A-L Barab\u00e1si","year":"2011","unstructured":"Barab\u00e1si A-L, Gulbahce N, Loscalzo J (2011) Network medicine: a network-based approach to human disease. Nat Rev Genet 12:56\u201368","journal-title":"Nat Rev Genet"},{"key":"175_CR4","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1007\/978-1-4419-9863-7_1607","volume-title":"Encyclopedia of systems biology","author":"V Chelliah","year":"2013","unstructured":"Chelliah V, Laibe C, Le Nov\u00e8re N (2013) BioModels database: a repository of mathematical models of biological processes. In: Encyclopedia of systems biology. Springer, New York, NY, pp 134\u2013138"},{"key":"175_CR5","doi-asserted-by":"publisher","first-page":"3665","DOI":"10.1016\/j.febslet.2006.05.053","volume":"580","author":"KH Cho","year":"2006","unstructured":"Cho KH, Baek S, Sung MH (2006) Wnt pathway mutations selected by optimal beta-catenin signaling for tumorigenesis. FEBS Lett 580:3665\u20133670. \n                    https:\/\/doi.org\/10.1016\/j.febslet.2006.05.053","journal-title":"FEBS Lett"},{"key":"175_CR6","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1016\/j.tig.2014.06.003","volume":"30","author":"F Dietlein","year":"2014","unstructured":"Dietlein F, Thelen L, Reinhardt HC (2014) Cancer-specific defects in DNA repair pathways as targets for personalized therapeutic approaches. Trends Genet 30:326\u2013339","journal-title":"Trends Genet"},{"key":"175_CR7","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/0771-050X(80)90013-3","volume":"6","author":"JR Dormand","year":"1980","unstructured":"Dormand JR, Prince PJ (1980) A family of embedded Runge\u2013Kutta formulae. J Comput Appl Math 6:19\u201326","journal-title":"J Comput Appl Math"},{"key":"175_CR8","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/1752-0509-2-39","volume":"2","author":"A Drager","year":"2008","unstructured":"Drager A, Hassis N, Supper J, Schroder A, Zell A (2008) SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst Biol 2:39. \n                    https:\/\/doi.org\/10.1186\/1752-0509-2-39","journal-title":"BMC Syst Biol"},{"key":"175_CR9","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.pharmthera.2016.02.003","volume":"160","author":"NS Gavande","year":"2016","unstructured":"Gavande NS, VanderVere-Carozza PS, Hinshaw HD, Jalal SI, Sears CR, Pawelczak KS, Turchi JJ (2016) DNA repair targeted therapy: the past or future of cancer treatment? Pharmacol Ther 160:65\u201383. \n                    https:\/\/doi.org\/10.1016\/j.pharmthera.2016.02.003","journal-title":"Pharmacol Ther"},{"key":"175_CR10","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1016\/j.jtbi.2008.01.006","volume":"252","author":"A Goldbeter","year":"2008","unstructured":"Goldbeter A, Pourqui\u00e9 O (2008) Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J Theor Biol 252:574\u2013585","journal-title":"J Theor Biol"},{"key":"175_CR11","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1146\/annurev.genom.3.022502.103043","volume":"3","author":"WM Grady","year":"2002","unstructured":"Grady WM, Markowitz SD (2002) Genetic and epigenetic alterations in colon cancer. Ann Rev Genom Hum Genet 3:101\u2013128","journal-title":"Ann Rev Genom Hum Genet"},{"key":"175_CR12","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1055\/s-0029-1242458","volume":"22","author":"FA Haggar","year":"2009","unstructured":"Haggar FA, Boushey RP (2009) Colorectal cancer epidemiology: incidence, mortality, survival, and risk factors. Clin Colon Rectal Surg 22:191\u2013197 \n                    https:\/\/doi.org\/10.1055\/s-0029-1242458","journal-title":"Clin Colon Rectal Surg"},{"key":"175_CR13","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1007\/s11888-006-0002-2","volume":"2","author":"IM Hisamuddin","year":"2006","unstructured":"Hisamuddin IM, Yang VW (2006) Molecular genetics of colorectal cancer: an overview. Curr Colorectal Cancer Rep 2:53\u201359","journal-title":"Curr Colorectal Cancer Rep"},{"key":"175_CR14","doi-asserted-by":"publisher","first-page":"e0179888","DOI":"10.1371\/journal.pone.0179888","volume":"12","author":"G Hochman","year":"2017","unstructured":"Hochman G, Halevi-Tobias K, Kogan Y, Agur Z (2017) Extracellular inhibitors can attenuate tumorigenic Wnt pathway activity in adenomatous polyposis coli mutants: predictions of a validated mathematical model. PloS One 12:e0179888","journal-title":"PloS One"},{"key":"175_CR15","doi-asserted-by":"publisher","first-page":"20492","DOI":"10.3390\/ijms141020492","volume":"14","author":"MY Huang","year":"2013","unstructured":"Huang MY et al (2013) Significant overexpression of DVL1 in Taiwanese colorectal cancer patients with liver metastasis. Int J Mol Sci 14:20492\u201320507. \n                    https:\/\/doi.org\/10.3390\/ijms141020492","journal-title":"Int J Mol Sci"},{"key":"175_CR16","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1002\/0470857897.ch8","volume":"247","author":"M Kanehisa","year":"2002","unstructured":"Kanehisa M (2002) The KEGG database. Novartis Found Symp 247:91\u2013101 (discussion 101\u2013103, 119\u2013128, 244\u2013252)","journal-title":"Novartis Found Symp"},{"key":"175_CR17","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1007\/s12015-007-0006-6","volume":"3","author":"M Katoh","year":"2007","unstructured":"Katoh M (2007) Networking of WNT, FGF, Notch, BMP, and Hedgehog signaling pathways during carcinogenesis. Stem Cell Rev 3:30\u201338","journal-title":"Stem Cell Rev"},{"key":"175_CR18","doi-asserted-by":"publisher","first-page":"1333","DOI":"10.1098\/rstb.2007.2251","volume":"363","author":"HA Kestler","year":"2008","unstructured":"Kestler HA, Kuhl M (2008) From individual Wnt pathways towards a Wnt signalling network philosophical transactions of the Royal Society of London Series B. Biol Sci 363:1333\u20131347. \n                    https:\/\/doi.org\/10.1098\/rstb.2007.2251","journal-title":"Biol Sci"},{"key":"175_CR19","first-page":"138","volume":"15","author":"R Kruger","year":"2004","unstructured":"Kruger R, Heinrich R (2004) Model reduction and analysis of robustness for the Wnt\/beta-catenin signal transduction pathway. Genome Inf Int Conf Genome Inf 15:138\u2013148","journal-title":"Genome Inf Int Conf Genome Inf"},{"key":"175_CR20","doi-asserted-by":"publisher","first-page":"E10","DOI":"10.1371\/journal.pbio.0000010","volume":"1","author":"E Lee","year":"2003","unstructured":"Lee E, Salic A, Kruger R, Heinrich R, Kirschner MW (2003) The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biol 1:E10. \n                    https:\/\/doi.org\/10.1371\/journal.pbio.0000010","journal-title":"PLoS Biol"},{"key":"175_CR21","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1016\/j.molmed.2016.02.003","volume":"22","author":"SK Li","year":"2016","unstructured":"Li SK, Martin A (2016) Mismatch repair and colon cancer: mechanisms and therapies explored. Trends Mol Med 22:274\u2013289","journal-title":"Trends Mol Med"},{"key":"175_CR22","first-page":"405","volume-title":"Mathematical and statistical techniques for systems medicine: the Wnt signaling pathway as a case study. Systems medicine","author":"AL MacLean","year":"2016","unstructured":"MacLean AL, Harrington HA, Stumpf MP, Byrne HM (2016) Mathematical and statistical techniques for systems medicine: the Wnt signaling pathway as a case study. Systems medicine. Humana Press, New York, 405\u2013439"},{"key":"175_CR23","doi-asserted-by":"publisher","first-page":"2449","DOI":"10.1056\/NEJMra0804588","volume":"361","author":"SD Markowitz","year":"2009","unstructured":"Markowitz SD, Bertagnolli MM (2009) Molecular origins of cancer: molecular basis of colorectal cancer. N Engl J Med 361:2449\u20132460. \n                    https:\/\/doi.org\/10.1056\/NEJMra0804588","journal-title":"N Engl J Med"},{"key":"175_CR24","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/S1535-6108(03)00216-2","volume":"4","author":"GS Martin","year":"2003","unstructured":"Martin GS (2003) Cell signaling cancer. Cancer Cell 4:167\u2013174","journal-title":"Cancer Cell"},{"key":"175_CR25","volume-title":"MATLAB and statistics toolbox release 2012a","author":"MathWorks","year":"2012","unstructured":"MathWorks T (2012) MATLAB and statistics toolbox release 2012a. The MathWorks, Inc, Natick"},{"key":"175_CR26","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1007\/s00285-009-0262-y","volume":"60","author":"GR Mirams","year":"2010","unstructured":"Mirams GR, Byrne HM, King JR (2010) A multiple timescale analysis of a mathematical model of the Wnt\/\u03b2-catenin signalling pathway. J Math Biol 60:131\u2013160","journal-title":"J Math Biol"},{"key":"175_CR27","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1093\/hmg\/10.7.735","volume":"10","author":"P Peltomaki","year":"2001","unstructured":"Peltomaki P (2001) Deficient DNA mismatch repair: a common etiologic factor for colon cancer. Hum Mol Genet 10:735\u2013740","journal-title":"Hum Mol Genet"},{"key":"175_CR28","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1504\/IJCBDD.2012.049203","volume":"5","author":"S Saha","year":"2012","unstructured":"Saha S, Roman T, Galante A, Koyuturk M, Ewing RM (2012) Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks. Int J Comput Biol Drug Des 5:185\u2013205. \n                    https:\/\/doi.org\/10.1504\/IJCBDD.2012.049203","journal-title":"Int J Comput Biol Drug Des"},{"key":"175_CR29","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1136\/gut.2006.093310","volume":"56","author":"J Schneikert","year":"2007","unstructured":"Schneikert J, Behrens J (2007) The canonical Wnt signalling pathway and its APC partner in colon cancer development. Gut 56:417\u2013425. \n                    https:\/\/doi.org\/10.1136\/gut.2006.093310","journal-title":"Gut"},{"key":"175_CR30","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.gene.2015.03.075","volume":"564","author":"A Shukla","year":"2015","unstructured":"Shukla A, Sehgal M, Singh TR (2015) Hydroxymethylation and its potential implication in DNA repair system: a review and future perspectives. Gene 564:109\u2013118. \n                    https:\/\/doi.org\/10.1016\/j.gene.2015.03.075","journal-title":"Gene"},{"key":"175_CR31","doi-asserted-by":"publisher","first-page":"e0157031","DOI":"10.1371\/journal.pone.0157031","volume":"11","author":"A Shukla","year":"2016","unstructured":"Shukla A, Moussa A, Singh TR (2016) DREMECELS: a curated database for base excision and mismatch repair mechanisms associated human malignancies. PloS One 11:e0157031. \n                    https:\/\/doi.org\/10.1371\/journal.pone.0157031","journal-title":"PloS One"},{"key":"175_CR32","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.genrep.2018.03.009","volume":"11","author":"A Shukla","year":"2018","unstructured":"Shukla A, Yennamalli RM, Singh TR (2018) Network and structure based inference of functional single nucleotide polymorphisms associated with the TGF\u03b21 gene and its role in colorectal cancer (CRC). Gene Rep 11:131\u2013142","journal-title":"Gene Rep"},{"key":"175_CR33","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1089\/omi.2011.0011","volume":"15","author":"KC Sivakumar","year":"2011","unstructured":"Sivakumar KC, Dhanesh SB, Shobana S, James J, Mundayoor S (2011) A systems biology approach to model neural stem cell regulation by notch, shh, wnt, and EGF signaling pathways. Omics J Integr Biol 15:729\u2013737","journal-title":"Omics J Integr Biol"},{"key":"175_CR34","first-page":"659","volume":"11","author":"BG Smaglo","year":"2013","unstructured":"Smaglo BG, Marshall JL (2013) Microsatellite instability in colorectal cancer. Clin Adv Hematol Oncol H&O 11:659\u2013661","journal-title":"Clin Adv Hematol Oncol H&O"},{"key":"175_CR35","doi-asserted-by":"publisher","first-page":"e31882","DOI":"10.1371\/journal.pone.0031882","volume":"7","author":"CW Tan","year":"2012","unstructured":"Tan CW, Gardiner BS, Hirokawa Y, Layton MJ, Smith DW, Burgess AW (2012) Wnt signalling pathway parameters for mammalian cells. PloS One 7:e31882. \n                    https:\/\/doi.org\/10.1371\/journal.pone.0031882","journal-title":"PloS One"},{"key":"175_CR36","doi-asserted-by":"publisher","first-page":"120","DOI":"10.28092\/j.issn.2095-3941.2015.0103","volume":"13","author":"K Tariq","year":"2016","unstructured":"Tariq K, Ghias K (2016) Colorectal cancer carcinogenesis: a review of mechanisms. Cancer Biol Med 13:120\u2013135. \n                    https:\/\/doi.org\/10.28092\/j.issn.2095-3941.2015.0103","journal-title":"Cancer Biol Med"},{"key":"175_CR37","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.jtbi.2007.01.019","volume":"247","author":"IM Leeuwen van","year":"2007","unstructured":"van Leeuwen IM, Byrne HM, Jensen OE, King JR (2007) Elucidating the interactions between the adhesive and transcriptional functions of \u03b2-catenin in normal and cancerous cells. J Theor Biol 247:77\u2013102","journal-title":"J Theor Biol"},{"key":"175_CR38","doi-asserted-by":"publisher","first-page":"1152","DOI":"10.1093\/bioinformatics\/btl038","volume":"22","author":"S Wernicke","year":"2006","unstructured":"Wernicke S, Rasche F (2006) FANMOD: a tool for fast network motif detection. Bioinformatics 22:1152\u20131153","journal-title":"Bioinformatics"},{"key":"175_CR39","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1002\/stem.2712","volume":"36","author":"MA Young","year":"2018","unstructured":"Young MA, Daly CS, Taylor E, James R, Clarke AR, Reed KR (2018) Subtle deregulation of the Wnt-signaling pathway through loss of Apc2 reduces the fitness of intestinal stem cells. Stem Cells 36:114\u2013122","journal-title":"Stem Cells"},{"key":"175_CR40","first-page":"144","volume":"8","author":"ZS Zeng","year":"2002","unstructured":"Zeng ZS, Shu WP, Cohen AM, Guillem JG (2002) Matrix metalloproteinase-7 expression in colorectal cancer liver metastases: evidence for involvement of MMP-7 activation in human cancer metastases. Clin Cancer Res 8:144\u2013148","journal-title":"Clin Cancer Res"},{"key":"175_CR41","doi-asserted-by":"publisher","first-page":"8836","DOI":"10.3748\/wjg.v21.i29.8836","volume":"21","author":"W Zhang","year":"2015","unstructured":"Zhang W et al (2015) Upregulation of nemo-like kinase is an independent prognostic factor in colorectal cancer. World J Gastroenterol WJG 21:8836","journal-title":"World J Gastroenterol WJG"}],"container-title":["Network Modeling Analysis in Health Informatics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s13721-018-0175-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-018-0175-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-018-0175-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T23:12:01Z","timestamp":1567811521000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s13721-018-0175-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,9,7]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["175"],"URL":"https:\/\/doi.org\/10.1007\/s13721-018-0175-z","relation":{},"ISSN":["2192-6662","2192-6670"],"issn-type":[{"value":"2192-6662","type":"print"},{"value":"2192-6670","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,9,7]]},"assertion":[{"value":"22 January 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 August 2018","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 September 2018","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 September 2018","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with ethical standards"}},{"value":"The authors declare that there are no conflicts of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"14"}}