Affiliations: Bioinformatics Team, Scientific and Engineering
Computing Group, Centre for Development of Advanced Computing, Pune University
Campus, Ganeshkhind, Pune, 411007, India. Tel.: +91 20 25694084; Fax: +91 20
25694081; E-mail: [email protected]
Note: [] Corresponding author
Abstract: The genes having similar expression profiles are considered to have
common regulatory mechanisms and are controlled by the binding of transcription
factors to the regulatory elements present in their upstream regions. The
detection of cis-regulatory elements can help in further understanding of
co-expression of genes. This paper deals with the detection of motifs in the
upstream regions of genes involved in diurnal rhythms of Arabidopsis and
also deals with the correlation of expression data with sequence information.
We detected motifs in the upstream regions of genes involved in diurnal cycles
and checked for their presence in circadian regulated, dark induced and in
light induced genes of Arabidopsis. Ten motifs were reported in this
study, out of which five were already reported in available transcription
factor databases as the elements involved in light responsiveness. Significance
study of ten motifs was done by taking random sets of same data size. One of
the ten motifs namely GGCCCA, which was found without any base variations in 62
genes, was further studied by analyzing the expression profiles of its
respective genes within the set of diurnal regulated genes using SOM clustering
method. It was found that the genes were clustered together into two major
groups, out of which one group had glycine rich proteins and the second group
had genes belonging to dehydrogenase and oxidoreductase family.
