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

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 , an R package for the systematic search for regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. mines multiple expression profiling datasets generated to test the same organism's response and identifies simple and composite regulatory elements systematically associated with differential expression of genes. Here, we showed performance for the identification of low-temperature-responsive regulatory code in and . identified potential binding sites for known as well as unknown cold response regulators. A notable part of elements was found in both searches discovering great conservation in low-temperature responses between plants and animals.