ArticleBioData mining2012
'MicroRNA Targets', a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana.
Article in BioData mining, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it, 25 citations in OpenAlex.
- Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.Plant physiology · 2013Pooled it
- TRUEE; a bioinformatic pipeline to define the functional microRNA targetome of Arabidopsis.The Plant journal : for cell and molecular biology · 2022Article
- ARGONAUTE1 and ARGONAUTE4 Regulate Gene Expression and Hypoxia Tolerance.Plant physiology · 2020Article
- Interplay between miRNA regulation and mechanical stress for CUC gene expression at the shoot apical meristem.Plant signaling & behavior · 2016Article
- A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.The Plant cell · 2014Article
- Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes.BMC genomics · 2014Article
- 'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences.Database : the journal of biological databases and curation · 2014Article
- Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection.PloS one · 2013Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe AthaMap database generates a genome-wide map for putative transcription factor binding sites for A. thaliana. When analyzing transcriptional regulation using AthaMap it may be important to learn which genes are also post-transcriptionally regulated by inhibitory RNAs. Therefore, a unified database for transcriptional and post-transcriptional regulation will be highly useful for the analysis of gene expression regulation.
methodsTo identify putative microRNA target sites in the genome of A. thaliana, processed mature miRNAs from 243 annotated miRNA genes were used for screening with the psRNATarget web server. Positional information, target genes and the psRNATarget score for each target site were annotated to the AthaMap database. Furthermore, putative target sites for small RNAs from seven small RNA transcriptome datasets were used to determine small RNA target sites within the A. thaliana genome.
resultsPutative 41,965 genome wide miRNA target sites and 10,442 miRNA target genes were identified in the A. thaliana genome. Taken together with genes targeted by small RNAs from small RNA transcriptome datasets, a total of 16,600 A. thaliana genes are putatively regulated by inhibitory RNAs. A novel web-tool, 'MicroRNA Targets', was integrated into AthaMap which permits the identification of genes predicted to be regulated by selected miRNAs. The predicted target genes are displayed with positional information and the psRNATarget score of the target site. Furthermore, putative target sites of small RNAs from selected tissue datasets can be identified with the new 'Small RNA Targets' web-tool.
conclusionsThe integration of predicted miRNA and small RNA target sites with transcription factor binding sites will be useful for AthaMap-assisted gene expression analysis. URL: http://www.athamap.de/
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Registered trials
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