IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner

Detalhes bibliográficos
Autor(a) principal: Vasconcelos, Ana M.
Data de Publicação: 2021
Outros Autores: Carmo, Maria Beatriz, Ferreira, Beatriz, Viegas, Inês, Gama‑Carvalho, Margarida, Ferreira, António, Amaral, Andreia J.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.5/24004
Resumo: Research Areas: Biochemistry & Molecular ; Biology Biotechnology & Applied ; Microbiology ; Mathematical & Computational Biology
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spelling IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly mannerIsomiRmiRNAAnnotation analysisFunctional analysisBrowser applicationResearch Areas: Biochemistry & Molecular ; Biology Biotechnology & Applied ; Microbiology ; Mathematical & Computational BiologyBackground: IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or more nucleotides (nts) at the 5′ and/or 3′ end, internal editings or untemplated 3′ end additions. Most available tools for small RNA-seq data analysis do not allow the identification of isomiRs and often require advanced knowledge of bioinformatics. To overcome this, we have developed IsomiR Window, a platform that supports the systematic identification, quantification and functional exploration of isomiR expression in small RNA-seq datasets, accessible to users with no computational skills. Methods: IsomiR Window enables the discovery of isomiRs and identification of all annotated non-coding RNAs in RNA-seq datasets from animals and plants. It comprises two main components: the IsomiR Window pipeline for data processing; and the IsomiR Window Browser interface. It integrates over ten third-party softwares for the analysis of small-RNA-seq data and holds a new algorithm that allows the detection of all possible types of isomiRs. These include 3′ and 5′end isomiRs, 3′ end tailings, isomiRs with single nucleotide polymorphisms (SNPs) or potential RNA editings, as well as all possible fuzzy combinations. IsomiR Window includes all required databases for analysis and annotation, and is freely distributed as a Linux virtual machine, including all required software. Results: IsomiR Window processes several datasets in an automated manner, without restrictions of input file size. It generates high quality interactive figures and tables which can be exported into different formats. The performance of isomiR detection and quantification was assessed using simulated small-RNA-seq data. For correctly mapped reads, it identified different types of isomiRs with high confidence and 100% accuracy. The analysis of a small RNA-seq data from Basal Cell Carcinomas (BCCs) using isomiR Window confirmed that miR-183-5p is up-regulated in Nodular BCCs, but revealed that this effect was predominantly due to a novel 5′end variant. This variant displays a different seed region motif and 1756 isoform-exclusive mRNA targets that are significantly associated with disease pathways, underscoring the biological relevance of isomiR-focused analysis. IsomiR Window is available at https ://isomi r.fc.ul.pt/.BMCRepositório da Universidade de LisboaVasconcelos, Ana M.Carmo, Maria BeatrizFerreira, BeatrizViegas, InêsGama‑Carvalho, MargaridaFerreira, AntónioAmaral, Andreia J.2022-04-04T15:03:15Z2021-02-012021-02-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.5/24004engVasconcelos AM, Carmo MB, Ferreira B, Viegas I, Gama-Carvalho M, Ferreira A, Amaral AJ. 2021. IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner. BMC Bioinformatics, 22(1):37. DOI 10.1186/s12859-021-03955-61471-210510.1186/s12859-021-03955-6info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-03-06T14:53:38Zoai:www.repository.utl.pt:10400.5/24004Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T17:08:08.644360Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
title IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
spellingShingle IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
Vasconcelos, Ana M.
IsomiR
miRNA
Annotation analysis
Functional analysis
Browser application
title_short IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
title_full IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
title_fullStr IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
title_full_unstemmed IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
title_sort IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner
author Vasconcelos, Ana M.
author_facet Vasconcelos, Ana M.
Carmo, Maria Beatriz
Ferreira, Beatriz
Viegas, Inês
Gama‑Carvalho, Margarida
Ferreira, António
Amaral, Andreia J.
author_role author
author2 Carmo, Maria Beatriz
Ferreira, Beatriz
Viegas, Inês
Gama‑Carvalho, Margarida
Ferreira, António
Amaral, Andreia J.
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Vasconcelos, Ana M.
Carmo, Maria Beatriz
Ferreira, Beatriz
Viegas, Inês
Gama‑Carvalho, Margarida
Ferreira, António
Amaral, Andreia J.
dc.subject.por.fl_str_mv IsomiR
miRNA
Annotation analysis
Functional analysis
Browser application
topic IsomiR
miRNA
Annotation analysis
Functional analysis
Browser application
description Research Areas: Biochemistry & Molecular ; Biology Biotechnology & Applied ; Microbiology ; Mathematical & Computational Biology
publishDate 2021
dc.date.none.fl_str_mv 2021-02-01
2021-02-01T00:00:00Z
2022-04-04T15:03:15Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.5/24004
url http://hdl.handle.net/10400.5/24004
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Vasconcelos AM, Carmo MB, Ferreira B, Viegas I, Gama-Carvalho M, Ferreira A, Amaral AJ. 2021. IsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly manner. BMC Bioinformatics, 22(1):37. DOI 10.1186/s12859-021-03955-6
1471-2105
10.1186/s12859-021-03955-6
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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