NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways Article Swipe
Zutan Li
,
Yuan Zhang
,
Jingya Fang
,
Zhihui Xu
,
Hao Zhang
,
Minfang Mao
,
Yuanyuan Chen
,
Liangyun Zhang
,
Cong Pian
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btac812
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btac812
Summary Non-coding RNAs play important roles in transcriptional processes and participate in the regulation of various biological functions, in particular miRNAs and lncRNAs. Despite their importance for several biological functions, the existing signaling pathway databases do not include information on miRNA and lncRNA. Here, we redesigned a novel pathway database named NcPath by integrating and visualizing a total of 178 308 human experimentally validated miRNA–target interactions (MTIs), 32 282 experimentally verified lncRNA–target interactions (LTIs) and 4837 experimentally validated human ceRNA networks across 222 KEGG pathways (including 27 sub-categories). To expand the application potential of the redesigned NcPath database, we identified 556 798 reliable lncRNA–protein-coding genes (PCG) interaction pairs by integrating co-expression relations, ceRNA relations, co-TF-binding interactions, co-histone-modification interactions, cis-regulation relations and lncPro Tool predictions between lncRNAs and PCG. In addition, to determine the pathways in which miRNA/lncRNA targets are involved, we performed a KEGG enrichment analysis using a hypergeometric test. The NcPath database also provides information on MTIs/LTIs/ceRNA networks, PubMed IDs, gene annotations and the experimental verification method used. In summary, the NcPath database will serve as an important and continually updated platform that provides annotation and visualization of the pathways on which non-coding RNAs (miRNA and lncRNA) are involved, and provide support to multimodal non-coding RNAs enrichment analysis. The NcPath database is freely accessible at http://ncpath.pianlab.cn/. Availability and implementation NcPath database is freely available at http://ncpath.pianlab.cn/. The code and manual to use NcPath can be found at https://github.com/Marscolono/NcPath/. Supplementary information Supplementary data are available at Bioinformatics online.
Related Topics
Concepts
KEGG
Competing endogenous RNA
microRNA
Computational biology
Visualization
Annotation
Computer science
Biology
Long non-coding RNA
Gene
RNA
Bioinformatics
Data mining
Genetics
Gene expression
Transcriptome
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btac812
- https://academic.oup.com/bioinformatics/article-pdf/39/1/btac812/48520847/btac812.pdf
- OA Status
- hybrid
- Cited By
- 40
- References
- 104
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4311678495
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4311678495Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/bioinformatics/btac812Digital Object Identifier
- Title
-
NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathwaysWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-12-16Full publication date if available
- Authors
-
Zutan Li, Yuan Zhang, Jingya Fang, Zhihui Xu, Hao Zhang, Minfang Mao, Yuanyuan Chen, Liangyun Zhang, Cong PianList of authors in order
- Landing page
-
https://doi.org/10.1093/bioinformatics/btac812Publisher landing page
- PDF URL
-
https://academic.oup.com/bioinformatics/article-pdf/39/1/btac812/48520847/btac812.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://academic.oup.com/bioinformatics/article-pdf/39/1/btac812/48520847/btac812.pdfDirect OA link when available
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KEGG, Competing endogenous RNA, microRNA, Computational biology, Visualization, Annotation, Computer science, Biology, Long non-coding RNA, Gene, RNA, Bioinformatics, Data mining, Genetics, Gene expression, TranscriptomeTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
40Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 13, 2024: 17, 2023: 9, 2022: 1Per-year citation counts (last 5 years)
- References (count)
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104Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.functions, | 18, 30 |
| abstract_inverted_index.identified | 100 |
| abstract_inverted_index.importance | 26 |
| abstract_inverted_index.multimodal | 205 |
| abstract_inverted_index.non-coding | 194, 206 |
| abstract_inverted_index.particular | 20 |
| abstract_inverted_index.redesigned | 46, 96 |
| abstract_inverted_index.regulation | 14 |
| abstract_inverted_index.relations, | 112, 114 |
| abstract_inverted_index.annotations | 163 |
| abstract_inverted_index.application | 92 |
| abstract_inverted_index.continually | 181 |
| abstract_inverted_index.information | 39, 156, 241 |
| abstract_inverted_index.integrating | 54, 110 |
| abstract_inverted_index.interaction | 107 |
| abstract_inverted_index.participate | 11 |
| abstract_inverted_index.predictions | 124 |
| abstract_inverted_index.visualizing | 56 |
| abstract_inverted_index.Availability | 218 |
| abstract_inverted_index.experimental | 166 |
| abstract_inverted_index.interactions | 66, 73 |
| abstract_inverted_index.miRNA/lncRNA | 137 |
| abstract_inverted_index.verification | 167 |
| abstract_inverted_index.Supplementary | 240, 242 |
| abstract_inverted_index.co-TF-binding | 115 |
| abstract_inverted_index.co-expression | 111 |
| abstract_inverted_index.interactions, | 116, 118 |
| abstract_inverted_index.visualization | 188 |
| abstract_inverted_index.Bioinformatics | 247 |
| abstract_inverted_index.cis-regulation | 119 |
| abstract_inverted_index.experimentally | 63, 70, 77 |
| abstract_inverted_index.hypergeometric | 149 |
| abstract_inverted_index.implementation | 220 |
| abstract_inverted_index.miRNA–target | 65 |
| abstract_inverted_index.MTIs/LTIs/ceRNA | 158 |
| abstract_inverted_index.lncRNA–target | 72 |
| abstract_inverted_index.transcriptional | 8 |
| abstract_inverted_index.sub-categories). | 88 |
| abstract_inverted_index.co-histone-modification | 117 |
| abstract_inverted_index.lncRNA–protein-coding | 104 |
| abstract_inverted_index.http://ncpath.pianlab.cn/. | 217, 227 |
| abstract_inverted_index.https://github.com/Marscolono/NcPath/. | 239 |
| cited_by_percentile_year.max | 100 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5100437877, https://openalex.org/A5024796378, https://openalex.org/A5028884115 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 9 |
| corresponding_institution_ids | https://openalex.org/I119454577, https://openalex.org/I4210096870 |
| citation_normalized_percentile.value | 0.95707444 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |