ArticleNucleic acids research2013
Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
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108 citing papers in PubMed.
- A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0.Bioinformatics (Oxford, England) · 2026Article
- Long Noncoding RNA function prediction via multiview cross-contrastive learning combined with multiscale semantic adaptive optimization.Briefings in bioinformatics · 2025Article
- Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer's Disease.International journal of molecular sciences · 2024Article
- Deciphering "Immaturity-Stemness" in Human Epidermal Stem Cells at the Levels of Protein-Coding and Non-Coding Genomes: A Prospective Computational Approach.International journal of molecular sciences · 2024Article
- Large-scale functional inference for skin-expressing lncRNAs using expression and sequence information.JCI insight · 2023Article
- Prediction of lncRNA functions using deep neural networks based on multiple networks.BMC genomics · 2023Article
- lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs.Database : the journal of biological databases and curation · 2023Article
- Genetic dissection of the impact of lncRNA AI662270 during the development of atherosclerosis.Journal of translational medicine · 2023Article
- EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.Briefings in bioinformatics · 2023Article
- Patterns of transcription factor binding and epigenome at promoters allow interpretable predictability of multiple functions of non-coding and coding genes.Computational and structural biotechnology journal · 2023Article
- Exploring the landscape of tools and resources for the analysis of long non-coding RNAs.Computational and structural biotechnology journal · 2023Review
- NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways.Bioinformatics (Oxford, England) · 2023Article
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- Designing libraries for pooled CRISPR functional screens of long noncoding RNAs.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma.Cellular oncology (Dordrecht, Netherlands) · 2022Article
- Hierarchical multi-label classification based on LSTM network and Bayesian decision theory for LncRNA function prediction.Scientific reports · 2022Article
- Ion channel long non-coding RNAs in neuropathic pain.Pflugers Archiv : European journal of physiology · 2022Review
- Construction of a Co-Expression Network for lncRNAs and mRNAs Related to Urothelial Carcinoma of the Bladder Progression.Frontiers in oncology · 2022Article
- Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer.Journal of translational medicine · 2021Article
48 more citing papers are in PubMed but not listed here.
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13 authors.
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No grant is acknowledged in the PubMed record.
Abstract
More and more evidences demonstrate that the long non-coding RNAs (lncRNAs) play many key roles in diverse biological processes. There is a critical need to annotate the functions of increasing available lncRNAs. In this article, we try to apply a global network-based strategy to tackle this issue for the first time. We develop a bi-colored network based global function predictor, long non-coding RNA global function predictor ('lnc-GFP'), to predict probable functions for lncRNAs at large scale by integrating gene expression data and protein interaction data. The performance of lnc-GFP is evaluated on protein-coding and lncRNA genes. Cross-validation tests on protein-coding genes with known function annotations indicate that our method can achieve a precision up to 95%, with a suitable parameter setting. Among the 1713 lncRNAs in the bi-colored network, the 1625 (94.9%) lncRNAs in the maximum connected component are all functionally characterized. For the lncRNAs expressed in mouse embryo stem cells and neuronal cells, the inferred putative functions by our method highly match those in the known literature.
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