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

2021-02-01Artigo científico Acesso aberto
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dc.contributor.authorVasconcelos, Ana M.
dc.contributor.authorCarmo, Maria Beatriz
dc.contributor.authorFerreira, Beatriz
dc.contributor.authorViegas, Inês
dc.contributor.authorGama‑Carvalho, Margarida
dc.contributor.authorFerreira, António
dc.contributor.authorAmaral, Andreia J.
dc.date.accessioned2022-04-04T15:03:15Z
dc.date.available2022-04-04T15:03:15Z
dc.date.issued2021-02-01
dc.descriptionResearch Areas: Biochemistry & Molecular ; Biology Biotechnology & Applied ; Microbiology ; Mathematical & Computational Biologypt_PT
dc.description.abstractBackground: 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/.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationVasconcelos 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/s12859-021-03955-6pt_PT
dc.identifier.doi10.1186/s12859-021-03955-6pt_PT
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/10400.5/24004
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherBMCpt_PT
dc.relationCentre for Interdisciplinary Research in Animal Health
dc.relationLASIGE - Extreme Computing
dc.relationLASIGE - Extreme Computing
dc.relation.publisherversionhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-03955-6pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectIsomiRpt_PT
dc.subjectmiRNApt_PT
dc.subjectAnnotation analysispt_PT
dc.subjectFunctional analysispt_PT
dc.subjectBrowser applicationpt_PT
dc.titleIsomiR_Window : a system for analyzing small‑RNA‑seq data in an integrative and user‑friendly mannerpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardNumberUIDB/00276/2020
oaire.awardNumberUIDB/00408/2020
oaire.awardNumberUIDP/00408/2020
oaire.awardNumberUID/Multi/04046/2013
oaire.awardNumberUID/CEC/00408/2013
oaire.awardTitleCentre for Interdisciplinary Research in Animal Health
oaire.awardTitleLASIGE - Extreme Computing
oaire.awardTitleLASIGE - Extreme Computing
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F00276%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F00408%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F00408%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FMulti%2F04046%2F2013/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FCEC%2F00408%2F2013/PT
oaire.citation.conferencePlaceLondon, Englandpt_PT
oaire.citation.titleBMC Bioinformaticspt_PT
oaire.citation.volume22(1):37pt_PT
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream5876
oaire.fundingStream5876
project.funder.identifierhttp://doi.org/10.13039/501100001871
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project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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