title: mirPRo-a novel standalone program for differential expression and variation analysis of miRNAs.
abstract: Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source standalone program (https://sourceforge.net/projects/mirpro/).
authors.affiliation: Department of Biology, Miami University and Center for Visual Sciences at Miami University, Oxford, Ohio 45056, USA.
authors.forename: Jieming
authors.initials: J
authors.lastname: Shi
authors.affiliation: Department of Biology, Miami University and Center for Visual Sciences at Miami University, Oxford, Ohio 45056, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Dong
authors.affiliation: Department of Biology, Miami University and Center for Visual Sciences at Miami University, Oxford, Ohio 45056, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Biology, Miami University and Center for Visual Sciences at Miami University, Oxford, Ohio 45056, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Biology, Miami University and Center for Visual Sciences at Miami University, Oxford, Ohio 45056, USA.|Department of Biology, University of Dayton and Center for Tissue Regeneration and Engineering at the University of Dayton (TREND), Dayton, Ohio 45469, USA.
authors.forename: Agustin
authors.initials: A
authors.lastname: Luz-Madrigal
authors.affiliation: Department of Biology, University of Dayton and Center for Tissue Regeneration and Engineering at the University of Dayton (TREND), Dayton, Ohio 45469, USA.
authors.forename: Panagiotis A
authors.initials: PA
authors.lastname: Tsonis
authors.affiliation: Department of Biology, Miami University and Center for Visual Sciences at Miami University, Oxford, Ohio 45056, USA.
authors.forename: Katia
authors.initials: K
authors.lastname: Del Rio-Tsonis
authors.affiliation: Department of Biology, Miami University and Center for Visual Sciences at Miami University, Oxford, Ohio 45056, USA.|Department of Computer Science and Software Engineering, Miami University, Oxford, Ohio 45056, USA.
authors.forename: Chun
authors.initials: C
authors.lastname: Liang
mesh_terms: D000818:Animals; D001483:Base Sequence; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome
chemical_list: D035683:MicroRNAs