Clustering Approach to Unveiling Relationships between Gene Regulatory Networks

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"> <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1, user-scalable=no"> <meta charset="utf-8"> <meta name="citation_title" content="Clustering Approach to Unveiling Relationships between Gene Regulatory Networks"> <meta name="citation_author" content="Hiba Hasan"> <meta name="citation_author" content="Khalid Raza"> <meta name="citation_publication_date" content="2013/09/03"> <meta name="citation_journal_title" content="International Journal of Computer and Information Engineering"> <meta name="citation_volume" content="6"> <meta name="citation_issue" content="5"> <meta name="citation_firstpage" content="739"> <meta name="citation_lastpage" content="742"> <meta name="citation_pdf_url" content="https://publications.waset.org/16904/pdf"> <link href="https://cdn.waset.org/favicon.ico" type="image/x-icon" rel="shortcut icon"> <link href="https://cdn.waset.org/static/plugins/bootstrap-4.2.1/css/bootstrap.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/plugins/fontawesome/css/all.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/css/site.css?v=150220211555" rel="stylesheet"> </head> <body> <header> <div class="container"> <nav class="navbar navbar-expand-lg navbar-light"> <a class="navbar-brand" href="https://waset.org"> <img src="https://cdn.waset.org/static/images/wasetc.png" alt="Open Science Research Excellence" title="Open Science Research Excellence" /> </a> <button class="d-block d-lg-none navbar-toggler ml-auto" type="button" data-toggle="collapse" data-target="#navbarMenu" aria-controls="navbarMenu" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div class="w-100"> <div class="d-none d-lg-flex flex-row-reverse"> <form method="get" action="https://waset.org/search" class="form-inline my-2 my-lg-0"> <input class="form-control mr-sm-2" type="search" placeholder="Search Conferences" value="" name="q" aria-label="Search"> <button class="btn btn-light my-2 my-sm-0" type="submit"><i class="fas fa-search"></i></button> </form> </div> <div class="collapse navbar-collapse mt-1" id="navbarMenu"> <ul class="navbar-nav ml-auto align-items-center" id="mainNavMenu"> <li class="nav-item"> <a class="nav-link" href="https://waset.org/conferences" title="Conferences in 2024/2025/2026">Conferences</a> </li> <li class="nav-item"> <a class="nav-link" href="https://waset.org/disciplines" title="Disciplines">Disciplines</a> </li> <li class="nav-item"> <a class="nav-link" href="https://waset.org/committees" rel="nofollow">Committees</a> </li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="navbarDropdownPublications" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> Publications </a> <div class="dropdown-menu" aria-labelledby="navbarDropdownPublications"> <a class="dropdown-item" href="https://publications.waset.org/abstracts">Abstracts</a> <a class="dropdown-item" href="https://publications.waset.org">Periodicals</a> <a class="dropdown-item" href="https://publications.waset.org/archive">Archive</a> </div> </li> <li class="nav-item"> <a class="nav-link" href="https://waset.org/page/support" title="Support">Support</a> </li> </ul> </div> </div> </nav> </div> </header> <main> <div class="container mt-4"> <div class="row"> <div class="col-md-9 mx-auto"> <form method="get" action="https://publications.waset.org/search"> <div id="custom-search-input"> <div class="input-group"> <i class="fas fa-search"></i> <input type="text" class="search-query" name="q" placeholder="Author, Title, Abstract, Keywords" value=""> <input type="submit" class="btn_search" value="Search"> </div> </div> </form> </div> </div> <div class="row mt-3"> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Commenced</strong> in January 2007</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Frequency:</strong> Monthly</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Edition:</strong> International</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Paper Count:</strong> 33093</div> </div> </div> </div> <div class="card publication-listing mt-3 mb-3"> <h5 class="card-header" style="font-size:.9rem">Clustering Approach to Unveiling Relationships between Gene Regulatory Networks</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/search?q=Hiba%20Hasan">Hiba Hasan</a>, <a href="https://publications.waset.org/search?q=Khalid%20Raza"> Khalid Raza</a> </p> <p class="card-text"><strong>Abstract:</strong></p> <p>Reverse engineering of genetic regulatory network involves the modeling of the given gene expression data into a form of the network. Computationally it is possible to have the relationships between genes, so called gene regulatory networks (GRNs), that can help to find the genomics and proteomics based diagnostic approach for any disease. In this paper, clustering based method has been used to reconstruct genetic regulatory network from time series gene expression data. Supercoiled data set from Escherichia coli has been taken to demonstrate the proposed method.</p> <iframe src="https://publications.waset.org/16904.pdf" style="width:100%; height:400px;" frameborder="0"></iframe> <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/search?q=Gene%20expression" title="Gene expression">Gene expression</a>, <a href="https://publications.waset.org/search?q=gene%20regulatory%20networks%20%28GRNs%29" title=" gene regulatory networks (GRNs)"> gene regulatory networks (GRNs)</a>, <a href="https://publications.waset.org/search?q=clustering" title=" clustering"> clustering</a>, <a href="https://publications.waset.org/search?q=data%20preprocessing" title=" data preprocessing"> data preprocessing</a>, <a href="https://publications.waset.org/search?q=network%20visualization." title=" network visualization. "> network visualization. </a> </p> <p class="card-text"><strong>Digital Object Identifier (DOI):</strong> <a href="https://doi.org/10.5281/zenodo.1088060" target="_blank">doi.org/10.5281/zenodo.1088060</a> </p> <a href="https://publications.waset.org/16904/clustering-approach-to-unveiling-relationships-between-gene-regulatory-networks" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/16904/apa" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">APA</a> <a href="https://publications.waset.org/16904/bibtex" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">BibTeX</a> <a href="https://publications.waset.org/16904/chicago" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">Chicago</a> <a href="https://publications.waset.org/16904/endnote" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">EndNote</a> <a href="https://publications.waset.org/16904/harvard" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">Harvard</a> <a href="https://publications.waset.org/16904/json" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">JSON</a> <a href="https://publications.waset.org/16904/mla" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">MLA</a> <a href="https://publications.waset.org/16904/ris" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">RIS</a> <a href="https://publications.waset.org/16904/xml" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">XML</a> <a href="https://publications.waset.org/16904/iso690" target="_blank" rel="nofollow" class="btn btn-primary btn-sm">ISO 690</a> <a href="https://publications.waset.org/16904.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">2152</span> </span> <p class="card-text"><strong>References:</strong></p> <br>[1] Helen C. Causton, John Quackenbush and Alvis Brazma, “A Beginner’s guide Microarray Gene Expression data Analysis,” Blackwell Publishing. <br>[2] K.H. Cho, S.M. Choo, S.H. Jung, J.R. Kim, H.S. Choi and J. Kim, “Reverse engineering of gene regulatory networks,” IET systems Biology, 2007, pp.149-163. <br>[3] Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu and Luonan Chen, “inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information,” Oxford university press. <br>[4] Shoudan Liang, Stefanie Fuhrman and Roland Somogyi, “REVEAL, A general reverse engineering algorithm for inferemce of genetic network architectures,” Pacific symposium on Biocomputing 3,1998, pp. 18-29. <br>[5] Khalid Raza and Rafat Parveen, "Evolutionary Algorithms in Genetic Regulatory Networks Model", Journal of Advanced Bioinformatics Applications and Research, 3(1):271-280, 2012. <br>[6] Xiaosheng Wang and Osamu Gotoh, “Inference of Cancer-speific gene Regulatory Networks Using Soft Computing Rules,” Gene Regulation and Systems Biology, 2010,19-34. <br>[7] Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke and Habtom w Ressom, “Reverse engineering module networks by PSORNN hybrid modeling,”, BMC Genomics, 2009. <br>[8] Brueckner F, Armache KJ, Cheung A, et al., "Structure–function studies of the RNA polymerase II elongation complex". Acta Crystallogr. D Biol. Crystallogr. 65 (Pt 2): 112–20, 2009 <br>[9] PP Amaral, ME Dinger, TR Mercer and JS Mattick, "The eukaryotic genome as an RNA machine". Science 319 (5871): 1787–9, 2008. <br>[10] B Schwanhäusser,D Busse, G Dittmar, J Schuchhardt, J Wolf, W Chen and M Selbach, "Global quantification of mammalian gene expression control". Nature 473 (7347): 337–42, 2011. <br>[11] Khalid Raza and Rafat Parveen, “Soft Computing Approach for Modeling Genetic Regulatory Networks”, 2nd International Conference on Artificial Intelligence, Soft Computing and Applications (AIAA- 2012), Proc. published in Advances in Intelligent Systems and Computing, AISC 178, pp 1-11, Springer-Verlag Berlin Heidelberg, 2012. <br>[12] Chesler EJ, Lu L, Wang J, Williams RW, Manly KF, "WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior". 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Clustering Approach to Unveiling Relationships between Gene Regulatory Networks