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In the first group, we assume that repressor and activator proteins compete for binding to the same regulatory site on DNA (competitive mechanisms). In the second group, they can bind to different regulatory regions in a noncompetitive fashion (noncompetitive mechanisms). For both competitive and noncompetitive mechanisms, we studied the gene expression dynamics by increasing the repressor or decreasing the activator abundance (inhibition mechanisms), or by decreasing the repressor or increasing the activator abundance (activation mechanisms). We employed delay differential equation models. Our simulation results show that the competitive and noncompetitive inhibition mechanisms exhibit comparable repression effectiveness. However, response time is fastest in the noncompetitive inhibition mechanism due to increased repressor abundance, and slowest in the competitive inhibition mechanism by increased repressor level. The competitive and noncompetitive inhibition mechanisms through decreased activator abundance show comparable and moderate response times, while the competitive and noncompetitive activation mechanisms by increased activator protein level display more effective and faster response. Our study exemplifies the importance of mathematical modeling and computer simulation in the analysis of gene expression dynamics.<\/jats:p>","DOI":"10.3233\/isb-160467","type":"journal-article","created":{"date-parts":[[2016,8,2]],"date-time":"2016-08-02T10:25:20Z","timestamp":1470133520000},"page":"95-127","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":1,"title":["Differential transcriptional regulation by\u00a0alternatively designed mechanisms: A\u00a0mathematical modeling approach"],"prefix":"10.1177","volume":"12","author":[{"given":"Necmettin","family":"Yildirim","sequence":"first","affiliation":[{"name":"Division of Natural Sciences, New College of Florida, Bayshore Road, Sarasota, FL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mehmet Emin","family":"Aktas","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Florida State University, W College Ave, 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