Correction to: NoRCE: non‑coding RNA sets cis enrichment tool

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buir.contributor.authorOlgun, Gülden
buir.contributor.orcidOlgun, Gülden|0000-0002-4467-1610
dc.citation.epage17en_US
dc.citation.issueNumber1en_US
dc.citation.spage1en_US
dc.citation.volumeNumber22en_US
dc.contributor.authorOlgun, Gülden
dc.contributor.authorNabi, Afshan
dc.contributor.authorTastan, Oznur
dc.date.accessioned2022-03-01T11:56:20Z
dc.date.available2022-02-11T08:23:44Z
dc.date.available2022-03-01T11:56:20Z
dc.date.issued2021-08-04
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractWhile some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results: We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions: NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.en_US
dc.identifier.doi10.1186/s12859-021-04112-9en_US
dc.identifier.eissn1471-2105
dc.identifier.urihttp://hdl.handle.net/11693/77269.2
dc.language.isoEnglishen_US
dc.publisherBioMed Central Ltd.en_US
dc.relation.isversionofhttps://doi.org/10.1186/s12859-021-04112-9en_US
dc.source.titleBMC Bioinformaticsen_US
dc.subjectNon-coding geneen_US
dc.subjectEnrichment analysisen_US
dc.subjectMulti-species R packageen_US
dc.subjectCo-expression analysisen_US
dc.subjectTADen_US
dc.titleCorrection to: NoRCE: non‑coding RNA sets cis enrichment toolen_US
dc.typeErratumen_US
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