Bioinformatic screening of the binding transcription sites in the regulatory regions of genes up-regulated in response to oxidative stress

Shkurat TP, Ponomareva NS, Aleksandrova AA, Shkurat MA, Butenko AI, Panich AE

Southern Federal University, Rostov-on-Don, Russia.

DOI: 10.4236/ojgen.2012.24B001                

Abstract

This study focuses on bioinformatics search for new regulatory structures in the non-coding DNA, located around the patterns of gene expression levels changed significantly in response to oxidative stress. Hypothesized that all of the genes increase the expression in response to oxidative stress may have the same motifs in non-coding DNA. To search for motifs created an integrated collection database of transcription binding sites - JASPAR, TRANSFAC, Hocomoco TF Homo sapiens, Uniprobe TF Mus musculus. Two types of regulatory regions: the promoter region and the sequence with the capture of potential cis-regulatory modules. In the regulatory regions of genes increase the expression in response to oxidative stress, in contrast to the gene expression level did not change, families of transcription factors identified SOX (1-30) and HX (A, B, C, D).

Keywords

Gene Expression; DNA Microarrays; Noncoding DNA; Oxidative Stress; Transcription Factor; Sites of Transcription Factor Binding; DNA Motif

Conflicts of Interest

The authors declare no conflicts of interest.

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