ArticleGenome biology2014
dCLIP: a computational approach for comparative CLIP-seq analyses.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed.
- Cerebellar microRNA-206 tunes Purkinje neuron firing dynamics to control sensorimotor gating.bioRxiv : the preprint server for biology · 2026Article
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.bioRxiv : the preprint server for biology · 2026Article
- DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.RNA biology · 2025Article
- Interplay of miR-243 and microbial interactions in aging and transgenerational immunity.Gut microbes · 2025Article
- Article
- PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.Methods in molecular biology (Clifton, N.J.) · 2022Article
- MicroRNA-directed pathway discovery elucidates an miR-221/222-mediated regulatory circuit in class switch recombination.The Journal of experimental medicine · 2021Article
- Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS.Nature communications · 2021Article
- Noncoding RNAs in B cell responses.RNA biology · 2021Review
- The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status.International journal of molecular sciences · 2021Review
- Techniques for Characterizing Cytomegalovirus-Encoded miRNAs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins.Quantitative biology (Beijing, China) · 2020Article
- RBinds: A user-friendly server for RNA binding site prediction.Computational and structural biotechnology journal · 2020Article
- PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks.PLoS computational biology · 2019Article
- Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.Methods (San Diego, Calif.) · 2019Review
- CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals.Nucleic acids research · 2018Article
- Recent computational developments on CLIP-seq data analysis and microRNA targeting implications.Briefings in bioinformatics · 2018Review
- uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins.Nature communications · 2018Article
- Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq.Nature communications · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/.
Indexed as
Identifiers
What OpenQuestion holds
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.