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

Abstract

Noncoding 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), 36,537 experimentally-verified lncRNA target interactions (LTIs), and 4,879 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 553,523 reliable lncRNA-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 protein-coding genes. In addition, to determine the pathways in which miRNA/lncRNA targets are involved, we performed a KEGG enrichment analysis using an 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 noncoding RNAs (miRNA and lncRNA) are involved, and provide support to multimodal noncoding RNAs enrichment analysis. The NcPath database is freely accessible at http://ncpath.pianlab.cn/.

Transcriptomic study reveals lncRNA-mediated downregulation of innate immune and inflammatory response in the SARS-CoV-2 vaccination breakthrough infections

“…The lncRNAs interacting with the mRNAs were used to perform Pathway enrichment analysis. ncPath web server was used to perform the pathway enrichment against KEGG database, and a cut-off of p-adj ≤ 0.05 was applied to select the significant pathways and was visualized using ggplot2 R package (25).…”

Comparative transcriptomic analysis of long noncoding RNAs in Leishmania-infected human macrophages

“…We used the NcPath’s ( Li et al, 2022 ) database of experimentally validated and predicted lncRNA-protein coding gene interaction to investigate these lncRNA targets by mechanisms other than cis regulation. To investigate their possible function, we submitted the putative target genes to Reactome enrichment of immune response-related pathways ( Table 2 ).…”

“…The Pearson correlation test (|R| > 0.8) was used to identify the association between 10 pairs of lncRNAs (BAALC-AS1, BAALC-AS2, HIF1A-AS1, HIF1A-AS3, TNFRSF14-AS1, IRF1-AS1, IL1R1-AS1, IL21R-AS1, RORA-AS1, and CA3-AS1) and mRNAs (BAALC, HIF1A, TNFRSF14, IRF1, IL1R1, IL21R, RORA, and CA3). These lncRNAs’ predicted targets were retrieved from the NcPath database ( Li et al, 2022 ) and submitted to GSEA based on Reactome gene sets for enrichment analysis.…”