ArticleBioinformatics (Oxford, England)2023
NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
28 citing papers in PubMed, 43 citations in OpenAlex.
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- Immune-Related Protein and Non-Coding RNA Cargo of Extracellular Vesicles Participate in the Chronic Inflammation Induced by HIV Infection.Journal of extracellular biology · 2025Article
- Machine learning and WGCNA reveal the PVT1/miR-143-3p/CDK1 ceRNA axis as a key regulator in NSCLC.Biochemistry and biophysics reports · 2025Article
- Manipulating PARK7/DJ-1 Levels by Genotoxic Stress Alters Noncoding RNAs and Cellular Homeostasis.Cells · 2025Article
- LncRNAs IFNG-AS1 and TH2LCRR as potential biomarkers of Th1/Th2 imbalance in diabetic nephropathy: From bioinformatics to experimental validation.Biochemistry and biophysics reports · 2025Article
- Deciphering the Diagnostic Potential of Small Non-Coding RNAs for the Detection of Pancreatic Ductal Adenocarcinoma Through Liquid Biopsies.International journal of molecular sciences · 2025Article
- lncRNAlyzr: Enrichment Analysis for lncRNA Sets.Journal of molecular biology · 2025Article
- Childhood Asthma Biomarkers Derived from Plasma and Saliva Exosomal miRNAs.International journal of molecular sciences · 2025Article
- Comparative Analysis of Differentially Expressed Long Non-Coding RNA in Pre- and Postmenopausal Fibroids.International journal of molecular sciences · 2025Article
- Long noncoding RNAs in acute myeloid leukemia: biomarkers, prognostic indicators, and treatment potential.Cancer cell international · 2025Review
- Advancing the therapeutic effectiveness of paclitaxel in chronic lymphocytic leukemia through the simultaneous inhibition of NOTCH1 and SF3B1.Cancer cell international · 2025Article
- Tissue levels of regulatory T cell related lncRNAs in lung cancer: evidence for dysregulation of immune responses.Discover oncology · 2025Article
- Spectral divergence prioritizes key classes, genes, and pathways shared between substance use disorders and cardiovascular disease.Frontiers in neuroscience · 2025Article
- Article
- Whole-blood RNA biomarkers for predicting survival in non-human primates following thoracic radiation.Scientific reports · 2024Article
- Article
- Nasopharyngeal airway long noncoding RNAs of infants with bronchiolitis and subsequent risk of developing childhood asthma.The Journal of allergy and clinical immunology · 2024Article
- Differential expression of angiogenesis-related genes 'VEGF' and 'angiopoietin-1' in metastatic and EMAST-positive colorectal cancer patients.Scientific reports · 2024Article
- Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers.Biomedicines · 2024Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
summaryNon-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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.