NcPath：一种用于可视化和富集分析人类非编码 RNA 和 KEGG 信号通路的新型平台。
NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways.
机构信息
College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
College of Science, Nanjing Agricultural University, Nanjing 210095, China.
出版信息
Bioinformatics. 2023 Jan 1;39(1). doi: 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.
摘要
非编码 RNA 在转录过程中发挥重要作用，并参与多种生物功能的调节，特别是 miRNA 和 lncRNA。尽管它们对许多生物功能很重要，但现有的信号通路数据库并不包含 miRNA 和 lncRNA 的信息。在这里，我们通过整合和可视化总共 178308 个人类实验验证的 miRNA-靶相互作用（MTI）、32282 个实验验证的 lncRNA-靶相互作用（LTI）和 4837 个实验验证的人类 ceRNA 网络，重新设计了一个名为 NcPath 的新型通路数据库，这些网络涉及 222 KEGG 通路（包括 27 个子类别）。为了扩展重新设计的 NcPath 数据库的应用潜力，我们通过整合共表达关系、ceRNA 关系、共 TF 结合相互作用、共组蛋白修饰相互作用、顺式调控关系和 lncPro Tool 预测，鉴定了 556798 个可靠的 lncRNA-编码基因（PCG）相互作用对之间的关系。此外，为了确定 miRNA/lncRNA 靶参与的通路，我们使用超几何检验进行了 KEGG 富集分析。NcPath 数据库还提供了 MTI/LTI/ceRNA 网络、PubMed ID、基因注释和使用的实验验证方法的信息。总之，NcPath 数据库将作为一个重要的、不断更新的平台，提供非编码 RNA（miRNA 和 lncRNA）参与的通路注释和可视化，并为多模态非编码 RNA 富集分析提供支持。NcPath 数据库可在 http://ncpath.pianlab.cn/ 免费访问。
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