Finding regulatory motif - (Nov/06/2006 )

Hello All,

We performed microarray experiment of two mutants and we are strongly suspicious that there is some regulatory motif that is present in the upregulated genes. I heard of few techniques where they took about 1kb of upstream regions from ATG, fed to some programs or home-grown bioinformatic methods and got some motif sequence, shown in the article as colorful image.

I am not at all a bioinformatician and have no idea of running a script. I will be happy if anybody could direct me to such programs or easy graphic unser interface methods.

I am searching on pubmed but all I am getting is very geeky stuff.

Many thanks for all inputs.

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Hi,

If you have the nucleotide sequences for the upregulated genes, you can use a program such as ClustalW (http://www.ebi.ac.uk/clustalw/) or T-Coffee (http://www.ebi.ac.uk/t-coffee/) to align and compare the sequences and look for any common motifs. But this will not specifically flag them as regulatory motifs...

Daz

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Hi, here is what you do:
1. get two lists of gene ids: mut1 and mut2
2. retrieve upstream 1000bp, 2000bp for both list
3. search for transcription factors binding sites in all sequences
4. perform chi-squre test to find statistical significant motif in both lists
5. examine and draw conclusion

If you think this is what you want, I can help you out step by step and help you to develop the tools and scripts.

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