NoRCE: non-coding RNA sets cis enrichment tool
Background: While 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 regulat...
Main Authors: | , , |
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Format: | Article |
Language: | English |
Published: |
BioMed Central Ltd
2021
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Online Access: | View Fulltext in Publisher |
LEADER | 03151nam a2200541Ia 4500 | ||
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001 | 10.1186-s12859-021-04112-9 | ||
008 | 220427s2021 CNT 000 0 und d | ||
020 | |a 14712105 (ISSN) | ||
245 | 1 | 0 | |a NoRCE: non-coding RNA sets cis enrichment tool |
260 | 0 | |b BioMed Central Ltd |c 2021 | |
856 | |z View Fulltext in Publisher |u https://doi.org/10.1186/s12859-021-04112-9 | ||
520 | 3 | |a Background: While 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. © 2021, The Author(s). | |
650 | 0 | 4 | |a animal |
650 | 0 | 4 | |a Animals |
650 | 0 | 4 | |a Cell culture |
650 | 0 | 4 | |a Co-expression |
650 | 0 | 4 | |a Co-expression analysis |
650 | 0 | 4 | |a Enrichment analysis |
650 | 0 | 4 | |a Expression data |
650 | 0 | 4 | |a Functional annotation |
650 | 0 | 4 | |a Functional associations |
650 | 0 | 4 | |a Functional genes |
650 | 0 | 4 | |a Genes |
650 | 0 | 4 | |a genetics |
650 | 0 | 4 | |a genome |
650 | 0 | 4 | |a Genome |
650 | 0 | 4 | |a Mammals |
650 | 0 | 4 | |a Mice |
650 | 0 | 4 | |a microRNA |
650 | 0 | 4 | |a MicroRNAs |
650 | 0 | 4 | |a Mirna target predictions |
650 | 0 | 4 | |a mouse |
650 | 0 | 4 | |a Multi-species R package |
650 | 0 | 4 | |a Non-coding gene |
650 | 0 | 4 | |a Non-coding RNAs |
650 | 0 | 4 | |a Platform independent |
650 | 0 | 4 | |a rat |
650 | 0 | 4 | |a Rats |
650 | 0 | 4 | |a RNA |
650 | 0 | 4 | |a RNA, Untranslated |
650 | 0 | 4 | |a TAD |
650 | 0 | 4 | |a untranslated RNA |
650 | 0 | 4 | |a zebra fish |
650 | 0 | 4 | |a Zebrafish |
700 | 1 | |a Nabi, A. |e author | |
700 | 1 | |a Olgun, G. |e author | |
700 | 1 | |a Tastan, O. |e author | |
773 | |t BMC Bioinformatics |