Cargando…

Using miRNA-Analyzer for the Analysis of miRNA Data

MicroRNAs (miRNAs) are small biological molecules that play an important role during the mechanisms of protein formation. Recent findings have demonstrated that they act as both positive and negative regulators of protein formation. Thus, the investigation of miRNAs, i.e., the determination of their...

Descripción completa

Detalles Bibliográficos
Autores principales: Guzzi, Pietro Hiram, Tradigo, Giuseppe, Veltri, Pierangelo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5197948/
https://www.ncbi.nlm.nih.gov/pubmed/27983673
http://dx.doi.org/10.3390/microarrays5040029
_version_ 1782488795537473536
author Guzzi, Pietro Hiram
Tradigo, Giuseppe
Veltri, Pierangelo
author_facet Guzzi, Pietro Hiram
Tradigo, Giuseppe
Veltri, Pierangelo
author_sort Guzzi, Pietro Hiram
collection PubMed
description MicroRNAs (miRNAs) are small biological molecules that play an important role during the mechanisms of protein formation. Recent findings have demonstrated that they act as both positive and negative regulators of protein formation. Thus, the investigation of miRNAs, i.e., the determination of their level of expression, has developed a huge interest in the scientific community. One of the leading technologies for extracting miRNA data from biological samples is the miRNA Affymetrix platform. It provides the quantification of the level of expression of the miRNA in a sample, thus enabling the accumulation of data and allowing the determination of relationships among miRNA, genes, and diseases. Unfortunately, there is a lack of a comprehensive platform able to provide all the functions needed for the extraction of information from miRNA data. We here present miRNA-Analyzer, a complete software tool providing primary functionalities for miRNA data analysis. The current version of miRNA-Analyzer wraps the Affymetrix QCTool for the preprocessing of binary data files, and then provides feature selection (the filtering by species and by the associated p-value of preprocessed files). Finally, preprocessed and filtered data are analyzed by the Multiple Experiment Viewer (T-MEV) and Short Time Series Expression Miner (STEM) tools, which are also wrapped into miRNA-Analyzer, thus providing a unique environment for miRNA data analysis. The tool offers a plug-in interface so it is easily extensible by adding other algorithms as plug-ins. Users may download the tool freely for academic use at https://sites.google.com/site/mirnaanalyserproject/d.
format Online
Article
Text
id pubmed-5197948
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-51979482017-01-04 Using miRNA-Analyzer for the Analysis of miRNA Data Guzzi, Pietro Hiram Tradigo, Giuseppe Veltri, Pierangelo Microarrays (Basel) Article MicroRNAs (miRNAs) are small biological molecules that play an important role during the mechanisms of protein formation. Recent findings have demonstrated that they act as both positive and negative regulators of protein formation. Thus, the investigation of miRNAs, i.e., the determination of their level of expression, has developed a huge interest in the scientific community. One of the leading technologies for extracting miRNA data from biological samples is the miRNA Affymetrix platform. It provides the quantification of the level of expression of the miRNA in a sample, thus enabling the accumulation of data and allowing the determination of relationships among miRNA, genes, and diseases. Unfortunately, there is a lack of a comprehensive platform able to provide all the functions needed for the extraction of information from miRNA data. We here present miRNA-Analyzer, a complete software tool providing primary functionalities for miRNA data analysis. The current version of miRNA-Analyzer wraps the Affymetrix QCTool for the preprocessing of binary data files, and then provides feature selection (the filtering by species and by the associated p-value of preprocessed files). Finally, preprocessed and filtered data are analyzed by the Multiple Experiment Viewer (T-MEV) and Short Time Series Expression Miner (STEM) tools, which are also wrapped into miRNA-Analyzer, thus providing a unique environment for miRNA data analysis. The tool offers a plug-in interface so it is easily extensible by adding other algorithms as plug-ins. Users may download the tool freely for academic use at https://sites.google.com/site/mirnaanalyserproject/d. MDPI 2016-12-15 /pmc/articles/PMC5197948/ /pubmed/27983673 http://dx.doi.org/10.3390/microarrays5040029 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Guzzi, Pietro Hiram
Tradigo, Giuseppe
Veltri, Pierangelo
Using miRNA-Analyzer for the Analysis of miRNA Data
title Using miRNA-Analyzer for the Analysis of miRNA Data
title_full Using miRNA-Analyzer for the Analysis of miRNA Data
title_fullStr Using miRNA-Analyzer for the Analysis of miRNA Data
title_full_unstemmed Using miRNA-Analyzer for the Analysis of miRNA Data
title_short Using miRNA-Analyzer for the Analysis of miRNA Data
title_sort using mirna-analyzer for the analysis of mirna data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5197948/
https://www.ncbi.nlm.nih.gov/pubmed/27983673
http://dx.doi.org/10.3390/microarrays5040029
work_keys_str_mv AT guzzipietrohiram usingmirnaanalyzerfortheanalysisofmirnadata
AT tradigogiuseppe usingmirnaanalyzerfortheanalysisofmirnadata
AT veltripierangelo usingmirnaanalyzerfortheanalysisofmirnadata