Identifying which promoters are regulating gene expression - (Oct/10/2011 )
I have microarray results showing a large number of significant changes in gene expression due to a treatment. I want to see whether there is any commonality between these genes in terms of particular transcription factors that may be activated by the treatment. One way to do this is to look for commonality in promoter regions. Is there any software or web resource that will search large numbers of significant genes from the microarray data and give results showing which promoters are most commonly found upstream of those genes?
are we talking about prokaryotic or eukaryotic transcriptomics?
For eukaryotes (human, mouse, drosophila, arabidopsis and s. cerevisiae) Pscan can be helpful to get a first idea. But you can only search certain regions (e.g. from -1000 to 0; from -200 to +50;...). You need RefSeq as input.