In Silico Analysis of Cis-Regulatory Elements on Co-Expressed Genes

Abstract

Cis-regulatory elements (CREs) are regions of non-coding DNA that regulate the transcription of nearby genes. CREs typically regulate gene transcription by functioning as binding sites for transcription factors. Publicly available database of co-expressed gene sets would be valuable tools for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. The study of CREs effect on expression can improve our understanding of co-expression genes and gene networks. In present study we compared the correlation between expression and CREs in co-expression genes with LTP5 by using the Genevestigator database that provides co-expressed genes deduced from microarray data, and SCOPE that uses to find CRDs in 800bp of upstream of the DNA sequences of co-expression genes. The result revealed that three motifs (TGSCAB, ATWTGYMG and CBTATC) of PRISM algorithm, GCCAC motif of BEAM and ATTGNVANNYGG motif of SPACER algorithm distribute in promoter of co-expressed genes and LUX transcription factor was identified by UniPROB database. We present here a new comparison method for detecting key cis-regulatory elements that effect on co-expressed genes to find a relation to clarify the function and regulation of particular genes and gene networks under stress conditions.