A novel pre-miRNA classification approach for the prediction of microRNA genes

MicroRNAs (miRNAs) are small non coding RNAs that play a significant role in gene regulation. Prediction of microRNA genes is a challenging bioinformatics problem. In our approach we applied an novel classification method, which combines the efficiency and robustness of Support Vector Machines with Genetic Algorithms for feature selection and parameters optimization. We tested our method with commonly used data and feature sets and we achieve higher performance in terms of sensitivity (99,10%), specificity (97,95%) and accuracy (98,68%) than the existing classifiers. Finally, we managed to extract a minimum subset consisted of 7 features that can standalone yield very high classification performance.

[1]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[2]  Vasile Palade,et al.  microPred: effective classification of pre-miRNAs for human miRNA gene prediction , 2009, Bioinform..

[3]  Weixiong Zhang,et al.  MicroRNA prediction with a novel ranking algorithm based on random walks , 2008, ISMB.

[4]  O. Maes,et al.  MicroRNA: Implications for Alzheimer Disease and other Human CNS Disorders , 2009, Current genomics.

[5]  Subbaya Subramanian,et al.  MicroRNAs as gatekeepers of apoptosis , 2010, Journal of cellular physiology.

[6]  Donna R. Maglott,et al.  RefSeq and LocusLink: NCBI gene-centered resources , 2001, Nucleic Acids Res..

[7]  S. Lowe,et al.  A microRNA polycistron as a potential human oncogene , 2005, Nature.

[8]  Stergios Papadimitriou,et al.  Efficient and interpretable fuzzy classifiers from data with support vector learning , 2005, Intell. Data Anal..

[9]  G Bernardi,et al.  CpG islands, genes and isochores in the genomes of vertebrates. , 1991, Gene.

[10]  Fei Li,et al.  Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine , 2005, BMC Bioinformatics.

[11]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature Reviews Genetics.

[12]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[13]  Peter F. Stadler,et al.  Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data , 2006, ISMB.

[14]  Chih-Jen Lin,et al.  Asymptotic Behaviors of Support Vector Machines with Gaussian Kernel , 2003, Neural Computation.

[15]  Michael T. McManus,et al.  Dysregulation of Cardiogenesis, Cardiac Conduction, and Cell Cycle in Mice Lacking miRNA-1-2 , 2007, Cell.

[16]  Habtom W. Ressom,et al.  Analysis of mass spectral serum profiles for biomarker selection , 2005, Bioinform..

[17]  Ashwin Srinivasan,et al.  Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM) , 2010, BMC Bioinformatics.

[18]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[19]  Jin-Wu Nam,et al.  Genomics of microRNA. , 2006, Trends in genetics : TIG.

[20]  B. Patterson,et al.  Letter to the editor. , 2018, Journal of professional nursing : official journal of the American Association of Colleges of Nursing.

[21]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[22]  Shobha Vasudevan,et al.  Cell cycle control of microRNA-mediated translation regulation , 2008, Cell cycle.

[23]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature reviews genetics.

[24]  Mihaela Zavolan,et al.  Identification of Clustered Micrornas Using an Ab Initio Prediction Method , 2022 .

[25]  Santosh K. Mishra,et al.  De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures , 2007, Bioinform..

[26]  S. Mishra,et al.  Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. , 2006, RNA.

[27]  K. J. Sweeney,et al.  MicroRNAs as Novel Biomarkers for Breast Cancer , 2009, Journal of oncology.

[28]  Nello Cristianini,et al.  Support vector machine classification and validation of cancer tissue samples using microarray expression data , 2000, Bioinform..

[29]  G. Rubin,et al.  Computational identification of Drosophila microRNA genes , 2003, Genome Biology.

[30]  Zissimos Mourelatos,et al.  The microRNA world: small is mighty. , 2003, Trends in biochemical sciences.

[31]  Byoung-Tak Zhang,et al.  Human microRNA prediction through a probabilistic co-learning model of sequence and structure , 2005, Nucleic acids research.

[32]  C. Burge,et al.  Vertebrate MicroRNA Genes , 2003, Science.

[33]  T. Tuschl,et al.  New microRNAs from mouse and human. , 2003, RNA.