ArticleRNA biology2015
SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins.
Article in RNA biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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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.
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Who cites it
9 citing papers in PubMed, 15 citations in OpenAlex.
- PTBP1 controls miRNA loading on target RNAs: lessons from the CyCoNP lncRNA.RNA (New York, N.Y.) · 2026Article
- Utilizing partial information decomposition to evaluate the complex interplay between microRNA and RNA-binding protein in regulating the shared target mRNA.Scientific reports · 2025Article
- MicroRNA Databases and Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Trends in the development of miRNA bioinformatics tools.Briefings in bioinformatics · 2019Review
- Antagonism between the RNA-binding protein Musashi1 and miR-137 and its potential impact on neurogenesis and glioblastoma development.RNA (New York, N.Y.) · 2019Article
- PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs.Nature communications · 2018Article
- Ancient and modern: hints of a core post-transcriptional network driving chemotherapy resistance in ovarian cancer.Wiley interdisciplinary reviews. RNA · 2018Review
- Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.PLoS computational biology · 2017Article
- Guardian of Genetic Messenger-RNA-Binding Proteins.Biomolecules · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 5 institutions in 5 countries.
Funding
Abstract
microRNAs and microRNA-independent RNA-binding proteins are 2 classes of post-transcriptional regulators that have been shown to cooperate in gene-expression regulation. We compared the genome-wide target sets of microRNAs and RBPs identified by recent CLIP-Seq technologies, finding that RBPs have distinct target sets and favor gene interaction network hubs. To identify microRNAs and RBPs with a similar functional context, we developed simiRa, a tool that compares enriched functional categories such as pathways and GO terms. We applied simiRa to the known functional cooperation between Pumilio family proteins and miR-221/222 in the regulation of tumor supressor gene p27 and show that the cooperation is reflected by similar enriched categories but not by target genes. SimiRa also predicts possible cooperation of microRNAs and RBPs beyond direct interaction on the target mRNA for the nuclear RBP TAF15. To further facilitate research into cooperation of microRNAs and RBPs, we made simiRa available as a web tool that displays the functional neighborhood and similarity of microRNAs and RBPs: http://vsicb-simira.helmholtz-muenchen.de.
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.