Finding differentially expressed sRNA-Seq regions with srnadiff.

Small RNAs (sRNAs) encompass a great variety of molecules of different kinds, such as microRNAs, small interfering RNAs, Piwi-associated RNA, among others. These sRNAs have a wide range of activities, which include gene regulation, protection against virus, transposable element silencing, and have b...

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Autores principales:	Matthias Zytnicki, Ignacio González
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0761803ef67c44438970e24f77483f72
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id	oai:doaj.org-article:0761803ef67c44438970e24f77483f72
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spelling	oai:doaj.org-article:0761803ef67c44438970e24f77483f722021-12-02T20:17:42ZFinding differentially expressed sRNA-Seq regions with srnadiff.1932-620310.1371/journal.pone.0256196https://doaj.org/article/0761803ef67c44438970e24f77483f722021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0256196https://doaj.org/toc/1932-6203Small RNAs (sRNAs) encompass a great variety of molecules of different kinds, such as microRNAs, small interfering RNAs, Piwi-associated RNA, among others. These sRNAs have a wide range of activities, which include gene regulation, protection against virus, transposable element silencing, and have been identified as a key actor in determining the development of the cell. Small RNA sequencing is thus routinely used to assess the expression of the diversity of sRNAs, usually in the context of differentially expression, where two conditions are compared. Tools that detect differentially expressed microRNAs are numerous, because microRNAs are well documented, and the associated genes are well defined. However, tools are lacking to detect other types of sRNAs, which are less studied, and whose precursor RNA is not well characterized. We present here a new method, called srnadiff, which finds all kinds of differentially expressed sRNAs. To the extent of our knowledge, srnadiff is the first tool that detects differentially expressed sRNAs without the use of external information, such as genomic annotation or additional sequences of sRNAs.Matthias ZytnickiIgnacio GonzálezPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 8, p e0256196 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Matthias Zytnicki Ignacio González Finding differentially expressed sRNA-Seq regions with srnadiff.
description	Small RNAs (sRNAs) encompass a great variety of molecules of different kinds, such as microRNAs, small interfering RNAs, Piwi-associated RNA, among others. These sRNAs have a wide range of activities, which include gene regulation, protection against virus, transposable element silencing, and have been identified as a key actor in determining the development of the cell. Small RNA sequencing is thus routinely used to assess the expression of the diversity of sRNAs, usually in the context of differentially expression, where two conditions are compared. Tools that detect differentially expressed microRNAs are numerous, because microRNAs are well documented, and the associated genes are well defined. However, tools are lacking to detect other types of sRNAs, which are less studied, and whose precursor RNA is not well characterized. We present here a new method, called srnadiff, which finds all kinds of differentially expressed sRNAs. To the extent of our knowledge, srnadiff is the first tool that detects differentially expressed sRNAs without the use of external information, such as genomic annotation or additional sequences of sRNAs.
format	article
author	Matthias Zytnicki Ignacio González
author_facet	Matthias Zytnicki Ignacio González
author_sort	Matthias Zytnicki
title	Finding differentially expressed sRNA-Seq regions with srnadiff.
title_short	Finding differentially expressed sRNA-Seq regions with srnadiff.
title_full	Finding differentially expressed sRNA-Seq regions with srnadiff.
title_fullStr	Finding differentially expressed sRNA-Seq regions with srnadiff.
title_full_unstemmed	Finding differentially expressed sRNA-Seq regions with srnadiff.
title_sort	finding differentially expressed srna-seq regions with srnadiff.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/0761803ef67c44438970e24f77483f72
work_keys_str_mv	AT matthiaszytnicki findingdifferentiallyexpressedsrnaseqregionswithsrnadiff AT ignaciogonzalez findingdifferentiallyexpressedsrnaseqregionswithsrnadiff
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Finding differentially expressed sRNA-Seq regions with srnadiff.

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