Preprint Article Version 1 This version is not peer-reviewed

metaRE R Package for Meta-analysis of Transcriptome Data to Identify the Cis-regulatory Code behind the Transcriptional Reprogramming

Version 1 : Received: 12 May 2020 / Approved: 13 May 2020 / Online: 13 May 2020 (15:17:16 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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.

Journal reference: Genes 2020, 11, 634
DOI: 10.3390/genes11060634

Abstract

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. Synergistic action of multiple pathways greatly complicates the experimental study of the molecular genetic mechanisms of the organism's reactions. As a result, 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 identification of cold stress-responsive cis-regulatory code in Arabidopsis thaliana. MetaRE identified potential binding sites for known as well as unknown cold response regulators. Software with source files, documentation, and example data files are freely available online at the repository (https://github.com/cheburechko/MetaRE).

Subject Areas

meta-analysis; transcription factor; binding site; genomics; transcriptomics; chilling stress; CBF; DREB; CAMTA

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