ArticleBMC genomics2012
Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 35 citations in OpenAlex.
- Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis.Genomics, proteomics & bioinformatics · 2022Article
- A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans.Frontiers in plant science · 2022Article
- Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum.BMC genomics · 2020Article
- Genome wide in-silico miRNA and target network prediction from stress responsive Horsegram (Macrotyloma uniflorum) accessions.Scientific reports · 2020Article
- miRNAs involved in transcriptome remodeling during pollen development and heat stress response in Solanum lycopersicum.Scientific reports · 2020Article
- PAREameters: a tool for computational inference of plant miRNA-mRNA targeting rules using small RNA and degradome sequencing data.Nucleic acids research · 2020Article
- Article
- PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules.Nucleic acids research · 2018Article
- Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis.The Plant cell · 2017Article
- Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.The Plant cell · 2016Review
- Heat Stress Affects Pi-related Genes Expression and Inorganic Phosphate Deposition/Accumulation in Barley.Frontiers in plant science · 2016Article
- Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica.Genome biology and evolution · 2015Article
- The evolution of the coding exome of the Arabidopsis species--the influences of DNA methylation, relative exon position, and exon length.BMC evolutionary biology · 2014Article
- Plant microRNA-target interaction identification model based on the integration of prediction tools and support vector machine.PloS one · 2014Article
- Article
- Biogenesis, turnover, and mode of action of plant microRNAs.The Plant cell · 2013Review
- Finding microRNA targets in plants: current status and perspectives.Genomics, proteomics & bioinformatics · 2012Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. Confident identification of MiRNA-Target Interactions (MTI) is vital to understand their function. Currently, several integrated computational programs and databases are available for animal miRNAs, the mechanisms of which are significantly different from plant miRNAs.
methodsHere we present an integrated MTI prediction and analysis toolkit (imiRTP) for Arabidopsis thaliana. It features two important functions: (i) combination of several effective plant miRNA target prediction methods provides a sufficiently large MTI candidate set, and (ii) different filters allow for an efficient selection of potential targets. The modularity of imiRTP enables the prediction of high quality targets on genome-wide scale. Moreover, predicted MTIs can be presented in various ways, which allows for browsing through the putative target sites as well as conducting simple and advanced analyses.
resultsResults show that imiRTP could always find high quality candidates compared with single method by choosing appropriate filter and parameter. And we also reveal that a portion of plant miRNA could bind target genes out of coding region. Based on our results, imiRTP could facilitate the further study of Arabidopsis miRNAs in real use. All materials of imiRTP are freely available under a GNU license at (http://admis.fudan.edu.cn/projects/imiRTP.htm).
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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.