ArticleGenome biology2013
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Article in Genome biology, 2013. 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.
- The probability of edge existence due to node degree: a baseline for network-based predictions.GigaScience · 2024Article
- A double-negative feedback loop between miR319c and JAW-TCPs establishes growth pattern in incipient leaf primordia in Arabidopsis thaliana.PLoS genetics · 2023Article
- Construction of a TF-miRNA-gene feed-forward loop network predicts biomarkers and potential drugs for myasthenia gravis.Scientific reports · 2021Article
- Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant.Nucleic acids research · 2018Article
- IndeCut evaluates performance of network motif discovery algorithms.Bioinformatics (Oxford, England) · 2018Article
- Randomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks.Journal of integrative bioinformatics · 2017Article
- Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.The Plant cell · 2016Review
- Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.The Plant cell · 2014Article
- Using machine learning to identify disease-relevant regulatory RNAs.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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
WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical aspects of biological networks, including self-loops, large hubs, and target rearrangements. We validate WaRSwap on a newly inferred regulatory network from Arabidopsis thaliana, and compare outcomes on published Drosophila and human networks. Specifically, sustained input switches are among the few over-represented circuits across this diverse set of eukaryotes.
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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.