NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways

'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 178308 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 556798 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.

Automated summary

Non-coding RNAs, including miRNAs and lncRNAs, play crucial roles in transcriptional processes and regulation of various biological functions. However, existing signaling pathway databases lack information on these non-coding RNAs. In this study, a novel pathway database called NcPath was developed by integrating and visualizing experimentally validated miRNA-target interactions (MTIs) and lncRNA-target interactions (LTIs) across KEGG pathways. Additionally, reliable lncRNA-protein-coding gene (PCG) interaction pairs were identified to expand the usability of the database. Overall, the NcPath database provides valuable annotation and visualization of the involvement of non-coding RNAs in pathways, supporting multimodal enrichment analysis.