title: Bioinformatic tools for microRNA dissection.
abstract: Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks. MiRNAs are endogenous single-stranded non-coding RNAs (~22-nt long) that regulate gene expression at the post-transcriptional level. Through pairing with mRNA, miRNAs can down-regulate gene expression by inhibiting translation or stimulating mRNA degradation. In some cases they can also up-regulate the expression of a target gene. MiRNAs influence a variety of cellular pathways that range from development to carcinogenesis. The involvement of miRNAs in several human diseases, particularly cancer, makes them potential diagnostic and prognostic biomarkers. Recent technological advances, especially high-throughput sequencing, have led to an exponential growth in the generation of miRNA-related data. A number of bioinformatic tools and databases have been devised to manage this growing body of data. We analyze 129 miRNA tools that are being used in diverse areas of miRNA research, to assist investigators in choosing the most appropriate tools for their needs.
authors.affiliation: Laboratory of Experimental Pathology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60100, Italy Computational Pathology Unit, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60100, Italy mauluda82@gmail.com.
authors.forename: Most Mauluda
authors.initials: MM
authors.lastname: Akhtar
authors.affiliation: Laboratory of Experimental Pathology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60100, Italy Computational Pathology Unit, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60100, Italy.
authors.forename: Luigina
authors.initials: L
authors.lastname: Micolucci
authors.affiliation: Department of Experimental and Clinical Medicine, Faculty of Medicine, Università Politecnica delle Marche, Ancona 60100, Italy.
authors.forename: Md Soriful
authors.initials: MS
authors.lastname: Islam
authors.affiliation: Laboratory of Experimental Pathology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60100, Italy Center of Clinical Pathology and Innovative Therapies, Italian National Research Center on Aging (INRCA-IRCCS), Ancona 60121, Italy.
authors.forename: Fabiola
authors.initials: F
authors.lastname: Olivieri
authors.affiliation: Laboratory of Experimental Pathology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60100, Italy Center of Clinical Pathology and Innovative Therapies, Italian National Research Center on Aging (INRCA-IRCCS), Ancona 60121, Italy.
authors.forename: Antonio Domenico
authors.initials: AD
authors.lastname: Procopio
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D059647:Gene-Environment Interaction; D020022:Genetic Predisposition to Disease; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism / Q000627:therapeutic use; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012106:Research
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger