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Open AccessArticle

metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming

1
Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia
2
Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
3
Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia
*
Author to whom correspondence should be addressed.
Genes 2020, 11(6), 634; https://doi.org/10.3390/genes11060634
Received: 12 May 2020 / Revised: 1 June 2020 / Accepted: 5 June 2020 / Published: 9 June 2020
At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. A significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism’s response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here, we showed metaRE performance for the identification of low-temperature-responsive cis-regulatory code in Arabidopsis thaliana and Danio rerio. MetaRE identified potential binding sites for known as well as unknown cold response regulators. A notable part of cis-elements was found in both searches discovering great conservation in low-temperature responses between plants and animals. View Full-Text
Keywords: meta-analysis; transcription factor; binding sites; genomics; transcriptomics; chilling stress; CBF; DREB; CAMTA1 meta-analysis; transcription factor; binding sites; genomics; transcriptomics; chilling stress; CBF; DREB; CAMTA1
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MDPI and ACS Style

Novikova, D.D.; Cherenkov, P.A.; Sizentsova, Y.G.; Mironova, V.V. metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming. Genes 2020, 11, 634. https://doi.org/10.3390/genes11060634

AMA Style

Novikova DD, Cherenkov PA, Sizentsova YG, Mironova VV. metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming. Genes. 2020; 11(6):634. https://doi.org/10.3390/genes11060634

Chicago/Turabian Style

Novikova, Daria D.; Cherenkov, Pavel A.; Sizentsova, Yana G.; Mironova, Victoria V. 2020. "metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming" Genes 11, no. 6: 634. https://doi.org/10.3390/genes11060634

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