ArticleGenome biology2017
Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- The role of RNA binding proteins in cancer biology: A focus on FMRP.Genes & diseases · 2025Review
- Loss of miRNA-Mediated VEGFA Regulation by SNP-Induced Impairment: A Bioinformatic Analysis in Diabetic Complications.Biomedicines · 2025Article
- Single cell multiomics reveals drivers of metabolic dysfunction-associated steatohepatitis.medRxiv : the preprint server for health sciences · 2025Article
- Systematic identification of post-transcriptional regulatory modules.Nature communications · 2024Article
- A Prognostic Methylation-Driven Two-Gene Signature in Medulloblastoma.Journal of molecular neuroscience : MN · 2024Article
- Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function.Development (Cambridge, England) · 2023Article
- A comparative atlas of single-cell chromatin accessibility in the human brain.Science (New York, N.Y.) · 2023Article
- Droplet-based single-cell joint profiling of histone modifications and transcriptomes.Nature structural & molecular biology · 2023Article
- Nucleotide-level prediction of CircRNA-protein binding based on fully convolutional neural network.Frontiers in genetics · 2023Article
- CRIT: Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization.Molecular therapy. Nucleic acids · 2022Article
- Survey of the binding preferences of RNA-binding proteins to RNA editing events.Genome biology · 2022Article
- Comprehensive characterization of posttranscriptional impairment-related 3'-UTR mutations in 2413 whole genomes of cancer patients.NPJ genomic medicine · 2022Article
- RBM47/SNHG5/FOXO3 axis activates autophagy and inhibits cell proliferation in papillary thyroid carcinoma.Cell death & disease · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Massively parallel reporter assays discover de novo exonic splicing mutants in paralogs of Autism genes.PLoS genetics · 2022Article
- A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation.Genome biology · 2021Article
- Article
- Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements.NAR genomics and bioinformatics · 2021Article
- The search for RNA-binding proteins: a technical and interdisciplinary challenge.Biochemical Society transactions · 2021Review
- NCBP3: A Multifaceted Adaptive Regulator of Gene Expression.Trends in biochemical sciences · 2021Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites. Such combinatorial clustering of RBPs helps interpret CLIP-seq data and suggests functional RNA regulatory elements. Furthermore, we validate two RBP-RBP interactions in cell lines. Our approach links proteins and RNA motifs known to possess similar biochemical and cellular properties and can, when used in conjunction with additional experimental data, identify high-confidence RBP groups and their associated RNA regulatory elements.
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