ArticleOncotarget2016
Subpathway-LNCE: Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies.
Article in Oncotarget, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Long non-coding RNAs in renal cell carcinoma: A systematic review and clinical implications.Oncotarget · 2017Pooled it
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- lncRNA LINC02323 predicts adverse neoadjuvant chemotherapy outcomes of gastric cancer patients and regulates cell sensitivity to 5-fluorouracil by negatively modulating miR-139-3p.Annals of medicine · 2024Article
- Inferring cell developmental stage-specific lncRNA regulation in the developing human neocortex with CDSlncR.Frontiers in molecular neuroscience · 2022Article
- Reconstruction and analysis of the aberrant lncRNA-miRNA-mRNA network based on competitive endogenous RNA in adenoid cystic carcinoma of the salivary gland.Translational cancer research · 2021Article
- Illuminating lncRNA Function Through Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Long noncoding RNA DLEU2 predicts a poor prognosis and enhances malignant properties in laryngeal squamous cell carcinoma through the miR-30c-5p/PIK3CD/Akt axis.Cell death & disease · 2020Article
- Construction of ceRNA Coexpression Network and Screening of Molecular Targets in Colorectal Cancer.Disease markers · 2020Article
- Topologically inferring active miRNA-mediated subpathways toward precise cancer classification by directed random walk.Molecular oncology · 2019Article
- Sub-pathway based approach to systematically track candidate sub-pathway biomarkers for heart failure.Experimental and therapeutic medicine · 2019Article
- Identification of lncRNA competitively regulated subpathways in myocardial infarction.Experimental and therapeutic medicine · 2019Article
- Abnormal sub-pathways competitively regulated by lncRNAs contribute to postmenopausal osteoporosis.Experimental and therapeutic medicine · 2019Article
- Microarray analysis reveals long non‑coding RNA SOX2OT as a novel candidate regulator in diabetic nephropathy.Molecular medicine reports · 2018Article
- Identification of pathways significantly associated with spondyloarthropathy/ankylosing spondylitis using the sub‑pathway method.Molecular medicine reports · 2018Article
- Inference of patient-specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer.Journal of cellular and molecular medicine · 2018Article
- Integrating gene and lncRNA expression to infer subpathway activity for tumor analyses.Oncotarget · 2017Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, studies have reported that long noncoding RNAs (lncRNAs) can act as modulators of mRNAs through competitively binding to microRNAs (miRNAs) and have relevance to tumorigenesis as well as other diseases. Identify lncRNA competitively regulated subpathway not only can gain insight into the initiation and progression of disease, but also help for understanding the functional roles of lncRNAs in the disease context. Here, we present an effective method, Subpathway-LNCE, which was specifically designed to identify lncRNAs competitively regulated functions and the functional roles of these competitive regulation lncRNAs have not be well characterized in diseases. Moreover, the method integrated lncRNA-mRNA expression profile and pathway topologies. Using prostate cancer datasets and LUAD data sets, we confirmed the effectiveness of our method in identifying disease associated dysfunctional subpathway that regulated by lncRNAs. By analyzing kidney renal clear cell carcinoma related lncRNA competitively regulated subpathway network, we show that Subpathway-LNCE can help uncover disease key lncRNAs. Furthermore, we demonstrated that our method is reproducible and robust. Subpathway-LNCE provide a flexible tool to identify lncRNA competitively regulated signal subpathways underlying certain condition, and help to expound the functional roles of lncRNAs in various status. Subpathway-LNCE has been developed as an R package freely available at https://cran.rstudio.com/web/packages/SubpathwayLNCE/.
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