title: HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens.
abstract: MiRNAs play an essential role in the networks of gene regulation by inhibiting the translation of target mRNAs. Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes. Thus, there is an imperative need to develop a computational method by which the target mRNAs of existing miRNAs can be correctly identified. In this study, combined pattern recognition neural network (PRNN) and principle component analysis (PCA) architecture has been proposed in order to model the complicated relationship between miRNAs and their target mRNAs in humans. The results of several types of intelligent classifiers and our proposed model were compared, showing that our algorithm outperformed them with higher sensitivity and specificity. Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select target candidates.
authors.affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors.forename: Hamed
authors.initials: H
authors.lastname: Ahmadi
authors.affiliation: Department of Electrical and Computer Engineering, Khajeh-Nasir Toosi University, Tehran, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Ahmadi
authors.affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors.forename: Sadegh
authors.initials: S
authors.lastname: Azimzadeh-Jamalkandi
authors.affiliation: Department of Mechatronics, Khajeh-Nasir Toosi University, Tehran, Iran.
authors.forename: Mahdi Aliyari
authors.initials: MA
authors.lastname: Shoorehdeli
authors.affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Salehzadeh-Yazdi
authors.affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors.forename: Gholamreza
authors.initials: G
authors.lastname: Bidkhori
authors.affiliation: Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. Electronic address: amasoudin@ibb.ut.ac.ir.
authors.forename: Ali
authors.initials: A
authors.lastname: Masoudi-Nejad
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008962:Models, Theoretical; D016571:Neural Networks, Computer; D010363:Pattern Recognition, Automated; D025341:Principal Component Analysis
chemical_list: D035683:MicroRNAs