Motif detection in Arabidopsis: correlation with gene expression data.
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.
Janaki
Chintalapati
C
Bioinformatics Team, Scientific and Engineering Computing Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India.
Joshi
Rajendra R
RR
D000465:Algorithms; D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D019992:Databases as Topic; D005786:Gene Expression Regulation; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D013997:Time Factors