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      Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls

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          Abstract

          Amyotrophic lateral sclerosis is a late-onset disorder primarily affecting motor neurons and leading to progressive and lethal skeletal muscle atrophy. Small RNAs, including microRNAs (miRNAs), can serve as important regulators of gene expression and can act both globally and in a tissue-/cell-type-specific manner. In muscle, miRNAs called myomiRs govern important processes and are deregulated in various disorders. Several myomiRs have shown promise for therapeutic use in cellular and animal models of ALS; however, the exact miRNA species differentially expressed in muscle tissue of ALS patients remain unknown. Following small RNA-Seq, we compared the expression of small RNAs in muscle tissue of ALS patients and healthy age-matched controls. The identified snoRNAs, mtRNAs and other small RNAs provide possible molecular links between insulin signaling and ALS. Furthermore, the identified miRNAs are predicted to target proteins that are involved in both normal processes and various muscle disorders and indicate muscle tissue is undergoing active reinnervation/compensatory attempts thus providing targets for further research and therapy development in ALS.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            MicroRNA profiling: approaches and considerations.

            MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate the expression of thousands of genes in a broad range of organisms in both normal physiological contexts and in disease contexts. miRNA expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and also show promise as biomarkers for disease. Technological advances have spawned a multitude of platforms for miRNA profiling, and an understanding of the strengths and pitfalls of different approaches can aid in their effective use. Here, we review the major considerations for carrying out and interpreting results of miRNA-profiling studies.
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              DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

              microRNAs (miRNAs) are short non-coding RNA species, which act as potent gene expression regulators. Accurate identification of miRNA targets is crucial to understanding their function. Currently, hundreds of thousands of miRNA:gene interactions have been experimentally identified. However, this wealth of information is fragmented and hidden in thousands of manuscripts and raw next-generation sequencing data sets. DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalog published experimentally validated miRNA:gene interactions. DIANA-TarBase v7.0 (http://www.microrna.gr/tarbase) aims to provide for the first time hundreds of thousands of high-quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data. DIANA-TarBase v7.0 enables users to easily identify positive or negative experimental results, the utilized experimental methodology, experimental conditions including cell/tissue type and treatment. The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments. More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database. DIANA-TarBase v7.0 is freely available.
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                Author and article information

                Contributors
                boris.rogelj@ijs.si
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                4 April 2018
                4 April 2018
                2018
                : 8
                : 5609
                Affiliations
                [1 ]ISNI 0000 0001 0706 0012, GRID grid.11375.31, Department of Biotechnology, , Jozef Stefan Institute, ; Jamova 39, Ljubljana, Slovenia
                [2 ]ISNI 0000 0004 0571 7705, GRID grid.29524.38, Institute of Clinical Neurophysiology, , Division of Neurology, University Medical Centre Ljubljana, ; Zaloška cesta 7, Ljubljana, Slovenia
                [3 ]ISNI 0000 0001 0721 6013, GRID grid.8954.0, Department of Neurology, Faculty of Medicine, , University of Ljubljana, ; Korytkova ulica 2, 1000 Ljubljana, Slovenia
                [4 ]ISNI 0000 0001 0721 6013, GRID grid.8954.0, University of Ljubljana, Faculty of Computer and Information Science, ; Večna pot 113, 1000 Ljubljana, Slovenia
                [5 ]Biomedical Research Institute BRIS, Ljubljana, 1000 Slovenia
                [6 ]ISNI 0000 0001 0721 6013, GRID grid.8954.0, Faculty of Chemistry and Chemical Technology, , University of Ljubljana, ; Večna pot 113, Ljubljana, 1000 Slovenia
                Author information
                http://orcid.org/0000-0003-4888-7256
                http://orcid.org/0000-0003-3898-1943
                Article
                23139
                10.1038/s41598-018-23139-2
                5884852
                29618798
                7b8c0e8c-26c3-4683-9ce0-6a54e117efe4
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 29 September 2017
                : 5 March 2018
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