ArticleSilence2013
cWords - systematic microRNA regulatory motif discovery from mRNA expression data.
Article in Silence, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 42 citations in OpenAlex.
- bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.Nucleic acids research · 2026Article
- Modulation of miR-29 influences myocardial compliance likely through coordinated regulation of calcium handling and extracellular matrix.Molecular therapy. Nucleic acids · 2023Article
- An unbiased seed-based RNAi selection screen identifies small RNAs that inhibit androgen signaling and prostate cancer cell growth.Molecular therapy. Nucleic acids · 2023Article
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- High-throughput identification of RNA localization elements in neuronal cells.Nucleic acids research · 2022Article
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- MicroRNA Targeting.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Seed-mediated RNA interference of androgen signaling and survival networks induces cell death in prostate cancer cells.Molecular therapy. Nucleic acids · 2021Article
- miRNA activity inferred from single cell mRNA expression.Scientific reports · 2021Article
- Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.Molecular cell · 2021Article
- High-Throughput Identification of MiR-145 Targets in Human Articular Chondrocytes.Life (Basel, Switzerland) · 2020Article
- The double edge of anti-CD40 siRNA therapy: It increases renal microcapillar density but favours the generation of an inflammatory milieu in the kidneys of ApoEJournal of inflammation (London, England) · 2019Article
- TGF-β induces miR-100 and miR-125b but blocks let-7a through LIN28B controlling PDAC progression.Nature communications · 2018Article
- Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.Algorithms for molecular biology : AMB · 2018Article
- Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.PLoS computational biology · 2017Article
- An overview of microRNAs.Advanced drug delivery reviews · 2015Review
- Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation.Genome biology · 2015Article
- Detection of miRNA regulatory effect on triple negative breast cancer transcriptome.BMC genomics · 2015Article
- Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data.Bioinformatics (Oxford, England) · 2014Article
- MixMir: microRNA motif discovery from gene expression data using mixed linear models.Nucleic acids research · 2014Article
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 at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPost-transcriptional regulation of gene expression by small RNAs and RNA binding proteins is of fundamental importance in development of complex organisms, and dysregulation of regulatory RNAs can influence onset, progression and potentially be target for treatment of many diseases. Post-transcriptional regulation by small RNAs is mediated through partial complementary binding to messenger RNAs leaving nucleotide signatures or motifs throughout the entire transcriptome. Computational methods for discovery and analysis of sequence motifs in high-throughput mRNA expression profiling experiments are becoming increasingly important tools for the identification of post-transcriptional regulatory motifs and the inference of the regulators and their targets.
resultscWords is a method designed for regulatory motif discovery in differential case-control mRNA expression datasets. We have improved the algorithms and statistical methods of cWords, resulting in at least a factor 100 speed gain over the previous implementation. On a benchmark dataset of 19 microRNA (miRNA) perturbation experiments cWords showed equal or better performance than two comparable methods, miReduce and Sylamer. We have developed rigorous motif clustering and visualization that accompany the cWords analysis for more intuitive and effective data interpretation. To demonstrate the versatility of cWords we show that it can also be used for identification of potential siRNA off-target binding. Moreover, cWords analysis of an experiment profiling mRNAs bound by Argonaute ribonucleoprotein particles discovered endogenous miRNA binding motifs.
conclusionscWords is an unbiased, flexible and easy-to-use tool designed for regulatory motif discovery in differential case-control mRNA expression datasets. cWords is based on rigorous statistical methods that demonstrate comparable or better performance than other existing methods. Rich visualization of results promotes intuitive and efficient interpretation of data. cWords is available as a stand-alone Open Source program at Github https://github.com/simras/cWords and as a web-service at: http://servers.binf.ku.dk/cwords/.
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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.