{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T23:39:15Z","timestamp":1783121955331,"version":"3.54.6"},"reference-count":98,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T00:00:00Z","timestamp":1671148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["JCQY202108"],"award-info":[{"award-number":["JCQY202108"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["ZJ22195010"],"award-info":[{"award-number":["ZJ22195010"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["KYCYXT2022010"],"award-info":[{"award-number":["KYCYXT2022010"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Startup Foundation for Advanced Talents at Nanjing Agricultural University","award":["050\/804009"],"award-info":[{"award-number":["050\/804009"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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\u200a308 human experimentally validated miRNA\u2013target interactions (MTIs), 32\u200a282 experimentally verified lncRNA\u2013target 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\u200a798 reliable lncRNA\u2013protein-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\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac812","type":"journal-article","created":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T18:12:08Z","timestamp":1671214328000},"source":"Crossref","is-referenced-by-count":37,"title":["NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways"],"prefix":"10.1093","volume":"39","author":[{"given":"Zutan","family":"Li","sequence":"first","affiliation":[{"name":"College of Agriculture, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Science, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingya","family":"Fang","sequence":"additional","affiliation":[{"name":"College of Agriculture, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihui","family":"Xu","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd. , Nanjing 210023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Science, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minfang","family":"Mao","sequence":"additional","affiliation":[{"name":"College of Science, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7953-1845","authenticated-orcid":false,"given":"Yuanyuan","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Science, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangyun","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Agriculture, Nanjing Agricultural University , Nanjing 210095, China"},{"name":"College of Science, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7401-2926","authenticated-orcid":false,"given":"Cong","family":"Pian","sequence":"additional","affiliation":[{"name":"College of Science, Nanjing Agricultural University , Nanjing 210095, China"},{"name":"The State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd. , Nanjing 210023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,16]]},"reference":[{"key":"2023010805411265100_btac812-B1","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1248\/bpb.29.903","article-title":"let-7 microRNA functions as a potential growth suppressor in human colon cancer cells","volume":"29","author":"Akao","year":"2006","journal-title":"Biol. 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