NoRCE: non-coding RNA sets cis enrichment tool
Abstract 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...
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| Format: | Article |
| Language: | English |
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BMC
2021-06-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-04112-9 |
| _version_ | 1819069597061480448 |
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| author | Gulden Olgun Afshan Nabi Oznur Tastan |
| author_facet | Gulden Olgun Afshan Nabi Oznur Tastan |
| author_sort | Gulden Olgun |
| collection | DOAJ |
| description | Abstract 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 . |
| first_indexed | 2024-12-21T16:52:34Z |
| format | Article |
| id | doaj.art-5ed31ff73b404f97aa3db98d7cfb59e2 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T16:52:34Z |
| publishDate | 2021-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-5ed31ff73b404f97aa3db98d7cfb59e22022-12-21T18:56:50ZengBMCBMC Bioinformatics1471-21052021-06-0122111710.1186/s12859-021-04112-9NoRCE: non-coding RNA sets cis enrichment toolGulden Olgun0Afshan Nabi1Oznur Tastan2Department of Computer Engineering, Bilkent UniversityFaculty of Engineering and Natural Sciences, Sabanci UniversityFaculty of Engineering and Natural Sciences, Sabanci UniversityAbstract 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 .https://doi.org/10.1186/s12859-021-04112-9Non-coding geneEnrichment analysisMulti-species R packageCo-expression analysisTAD |
| spellingShingle | Gulden Olgun Afshan Nabi Oznur Tastan NoRCE: non-coding RNA sets cis enrichment tool BMC Bioinformatics Non-coding gene Enrichment analysis Multi-species R package Co-expression analysis TAD |
| title | NoRCE: non-coding RNA sets cis enrichment tool |
| title_full | NoRCE: non-coding RNA sets cis enrichment tool |
| title_fullStr | NoRCE: non-coding RNA sets cis enrichment tool |
| title_full_unstemmed | NoRCE: non-coding RNA sets cis enrichment tool |
| title_short | NoRCE: non-coding RNA sets cis enrichment tool |
| title_sort | norce non coding rna sets cis enrichment tool |
| topic | Non-coding gene Enrichment analysis Multi-species R package Co-expression analysis TAD |
| url | https://doi.org/10.1186/s12859-021-04112-9 |
| work_keys_str_mv | AT guldenolgun norcenoncodingrnasetscisenrichmenttool AT afshannabi norcenoncodingrnasetscisenrichmenttool AT oznurtastan norcenoncodingrnasetscisenrichmenttool |