ArticlePLoS computational biology2020
LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Differential expression of NEAT1 and miR-506-3p in triple-negative breast cancer: potential tissue-based diagnostic biomarkers.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- Non-coding RNAs as a Critical Player in the Regulation of Inflammasome in Inflammatory Bowel Diseases; Emphasize on lncRNAs.Cell biochemistry and biophysics · 2025Review
- Dynamic role of long noncoding RNA in liver diseases: pathogenesis and diagnostic aspects.Clinical and experimental medicine · 2025Review
- Cardioprotection of voluntary exercise against breast cancer-induced cardiac injury via STAT3.Basic research in cardiology · 2025Article
- Modeling ncRNA Synergistic Regulation in Cancer.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Critical role of non-coding RNA-mediated ferroptosis in urologic malignancies.Frontiers in immunology · 2024Review
- Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers.PLoS computational biology · 2023Article
- Emerging RNA-Based Therapeutic and Diagnostic Options: Recent Advances and Future Challenges in Genitourinary Cancers.International journal of molecular sciences · 2023Review
- Methylated DNA markers for plasma detection of ovarian cancer: Discovery, validation, and clinical feasibility.Gynecologic oncology · 2022Article
- The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders.International journal of molecular sciences · 2022Review
- LncRNA MNX1-AS1 contributes to lung adenocarcinoma progression by targeting the miR-34a/SIRT1 axis.American journal of translational research · 2022Article
- Long Noncoding RNA Mediated Regulation in Human Embryogenesis, Pluripotency, and Reproduction.Stem cells international · 2022Review
- miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation.Bioinformatics advances · 2022Article
- Inferring miRNA sponge modules across major neuropsychiatric disorders.Frontiers in molecular neuroscience · 2022Article
- The Crosstalk of Long Non-Coding RNA and MicroRNA in Castration-Resistant and Neuroendocrine Prostate Cancer: Their Interaction and Clinical Importance.International journal of molecular sciences · 2021Review
- miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data.RNA biology · 2021Article
- LncRNAs and Immunity: Coding the Immune System with Noncoding Oligonucleotides.International journal of molecular sciences · 2021Review
- Expression Signatures of Long Noncoding RNAs in Left Ventricular Noncompaction.Frontiers in cardiovascular medicine · 2021Article
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Authors and funding
9 authors.
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Abstract
Until now, existing methods for identifying lncRNA related miRNA sponge modules mainly rely on lncRNA related miRNA sponge interaction networks, which may not provide a full picture of miRNA sponging activities in biological conditions. Hence there is a strong need of new computational methods to identify lncRNA related miRNA sponge modules. In this work, we propose a framework, LMSM, to identify LncRNA related MiRNA Sponge Modules from heterogeneous data. To understand the miRNA sponging activities in biological conditions, LMSM uses gene expression data to evaluate the influence of the shared miRNAs on the clustered sponge lncRNAs and mRNAs. We have applied LMSM to the human breast cancer (BRCA) dataset from The Cancer Genome Atlas (TCGA). As a result, we have found that the majority of LMSM modules are significantly implicated in BRCA and most of them are BRCA subtype-specific. Most of the mediating miRNAs act as crosslinks across different LMSM modules, and all of LMSM modules are statistically significant. Multi-label classification analysis shows that the performance of LMSM modules is significantly higher than baseline's performance, indicating the biological meanings of LMSM modules in classifying BRCA subtypes. The consistent results suggest that LMSM is robust in identifying lncRNA related miRNA sponge modules. Moreover, LMSM can be used to predict miRNA targets. Finally, LMSM outperforms a graph clustering-based strategy in identifying BRCA-related modules. Altogether, our study shows that LMSM is a promising method to investigate modular regulatory mechanism of sponge lncRNAs from heterogeneous data.
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