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

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. 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.

Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis

“…The inter-AuxRE spacer range was based on the maximum distance that could reasonably be expected to allow protein-protein interaction when two ARFs are bound. To evaluate the association of these composite elements with auxin responsiveness, we conducted a meta-analysis of publicly available transcriptomic datasets (5 RNA-Seq and 10 microarray datasets) related to auxin (listed in SI Appendix, Table S3) using the metaRE pipeline (53). For each dataset, we estimated statistically (Fisher's exact test) if any of the 33 AuxRE repeats (IR0-10, ER0-10, DR0-10) were enriched in upstream regions of auxin-dependent genes.…”

Identification of antineoplastic agents for oral squamous cell carcinoma: an integrated bioinformatics approach using differential gene expression and network biology

“…Several packages of R software i.e. MetaDE [51], MetaRE [52] and metaRNASeq [53] are available to perform meta-analysis of gene expression datasets. However due to the differences in the platform of the selected datasets, DEGs were initially filtered from each dataset based on adj.…”

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

“…For revealing specific motifs associated with selected DEGs in first stage, we used approach originally described in [34] and the package metaRE (Russia, Novosibirsk, https://github.com/cheburechko/metaRE, date of access 5 January 2022 [66]). Analysis algorithm included the following steps.…”