ArticlePLoS computational biology2018
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.
Article in PLoS computational biology, 2018. 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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Who cites it
18 citing papers in PubMed, 31 citations in OpenAlex.
- The metastasis landscape ofFrontiers in immunology · 2026Article
- Modeling ncRNA Synergistic Regulation in Cancer.Methods in molecular biology (Clifton, N.J.) · 2025Review
- LncRNA AFAP1-AS1 Promotes Oral Squamous Cell Carcinoma Development by Ubiquitin-Mediated Proteolysis.International dental journal · 2024Article
- Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks.BMC bioinformatics · 2024Article
- Systematic analysis identifies REST as an oncogenic and immunological biomarker in glioma.Scientific reports · 2023Article
- Integrative network analysis reveals subtype-specific long non-coding RNA regulatory mechanisms in head and neck squamous cell carcinoma.Computational and structural biotechnology journal · 2023Article
- iPiDA-GCN: Identification of piRNA-disease associations based on Graph Convolutional Network.PLoS computational biology · 2022Article
- A supervised machine learning approach identifies gene-regulating factor-mediated competing endogenous RNA networks in hormone-dependent cancers.Journal of cellular biochemistry · 2022Article
- Novel long noncoding RNA (lncRNA) panel as biomarkers for prognosis in lung squamous cell carcinoma via competitive endogenous RNA (ceRNA) network analysis.Translational cancer research · 2021Article
- An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions.PloS one · 2021Article
- Novel lncRNA Panel as for Prognosis in Esophageal Squamous Cell Carcinoma Based on ceRNA Network Mechanism.Computational and mathematical methods in medicine · 2021Article
- LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer.PLoS computational biology · 2020Article
- Multi-Omics Integration Reveals a Competitive Endogenous RNAs Network for the Identification of Progression Biomarkers and the Stratification of Patients Diagnosed With Nephroblastoma.Frontiers in oncology · 2020Article
- LncRNA TTN-AS1 promotes the progression of oral squamous cell carcinoma via miR-411-3p/NFAT5 axis.Cancer cell international · 2020Article
- LAceModule: Identification of Competing Endogenous RNA Modules by Integrating Dynamic Correlation.Frontiers in genetics · 2020Article
- Circulating non-coding RNAs in recurrent and metastatic ovarian cancer.Cancer drug resistance (Alhambra, Calif.) · 2019Review
- Identification of Dysregulated Competitive Endogenous RNA Networks Driven by Copy Number Variations in Malignant Gliomas.Frontiers in genetics · 2019Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) inhibit expression of target genes by binding to their RNA transcripts. It has been recently shown that RNA transcripts targeted by the same miRNA could "compete" for the miRNA molecules and thereby indirectly regulate each other. Experimental evidence has suggested that the aberration of such miRNA-mediated interaction between RNAs-called competing endogenous RNA (ceRNA) interaction-can play important roles in tumorigenesis. Given the difficulty of deciphering context-specific miRNA binding, and the existence of various gene regulatory factors such as DNA methylation and copy number alteration, inferring context-specific ceRNA interactions accurately is a computationally challenging task. Here we propose a computational method called Cancerin to identify cancer-associated ceRNA interactions. Cancerin incorporates DNA methylation, copy number alteration, gene and miRNA expression datasets to construct cancer-specific ceRNA networks. We applied Cancerin to three cancer datasets from the Cancer Genome Atlas (TCGA) project. Our results indicated that ceRNAs were enriched with cancer-related genes, and ceRNA modules in the inferred ceRNA networks were involved in cancer-associated biological processes. Using LINCS-L1000 shRNA-mediated gene knockdown experiment in breast cancer cell line to assess accuracy, Cancerin was able to predict expression outcome of ceRNA genes with high accuracy.
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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 OpenQuestion graph.