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

Abstract

Summary 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), 32,282 experimentally-verified lncRNA target interactions (LTIs), and 4,837 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-PCG (protein-coding genes) 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/. 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.

Differential expression of angiogenesis-related genes ‘VEGF’ and ‘angiopoietin-1’ in metastatic and EMAST-positive colorectal cancer patients

“…Finally, A competitive endogenous RNA (ceRNA) network encompassing ANGPT-1, ANGPT-2, and VEGF-A genes, experimentally validated TFs influencing these genes, experimentally validated miRNAs targeting selected genes, and experimentally validated lncRNAs targeting the validated miRNAs was constructed using Cytoscape software 33 . Furthermore, NcPath database was utilized to enrich the ceRNA network ( http://ncpath.pianlab.cn/#/Home ) 34 .…”

The impact of lncRNAs MIR503HG, TTN-AS1, and FEZF1-AS1 and their association with miR-107 expression in type 2 diabetes mellitus

“…NcPath is a novel visualization and enrichment analysis tool for non-coding RNA and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways in human, bridging the gap between biological pathways and human lncRNAs/miRNAs to enhance our understanding of lncRNAs/miRNAs function, particularly the investigation of the roles played by these types of RNAs in physiological and pathological processes [23]. To determine the pathways in which targets of a certain miRNA/lncRNA or multiple miRNAs/lncRNAs were enriched, NcPath performed a KEGG analysis by using the hypergeometric test.…”

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

“…We also analyzed lists of highly co-expressed genes retrieved regarding lincRNAs without differential expression in cancer types. Since plenty of co-expressed genes represented non-coding RNAs and pseudogenes, we used the NCpath web-based tool [ 46 ] adapted for functional enrichment analysis of gene sets containing non-coding RNAs. All the pathway terms are shown in Table S14 , and the most frequent pathway terms are summarized in Table S15 .…”