Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role
AuthorsKleftogiannis, Dimitrios A.
Theofilatos, Konstantinos A.
Likothanassis, Spiridon D.
Tsakalidis, Athanasios K.
Mavroudi, Seferina P.
KAUST DepartmentComputer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/566055
MetadataShow full item record
AbstractTraditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. © 2013 Elsevier Inc.
CitationKleftogiannis, D., Korfiati, A., Theofilatos, K., Likothanassis, S., Tsakalidis, A., & Mavroudi, S. (2013). Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. Journal of Biomedical Informatics, 46(3), 563–573. doi:10.1016/j.jbi.2013.02.002
SponsorsThis research has been co-financed by the European Union (European Social Fund - ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: Heracleitus II. Investing in knowledge society through the European Social Fund.
- Computational methods for microRNA target prediction.
- Authors: Watanabe Y, Tomita M, Kanai A
- Issue date: 2007
- Toward microRNA-mediated gene regulatory networks in plants.
- Authors: Meng Y, Shao C, Chen M
- Issue date: 2011 Nov
- Computational identification of microRNAs and their targets.
- Authors: Yoon S, De Micheli G
- Issue date: 2006 Jun
- Benchmark comparison of ab initio microRNA identification methods and software.
- Authors: Hu LL, Huang Y, Wang QC, Zou Q, Jiang Y
- Issue date: 2012 Dec 19
- Utilization of SSCprofiler to predict a new miRNA gene.
- Authors: Oulas A, Poirazi P
- Issue date: 2011