gene clustering using motif

asankaf · 07-17-2009, 01:19 AM

Hi,

I am new to molecular biology and I am going to cluster yeast gene using several data sources. I know that gene can be clustered using gene expression data and using other alternatives. I klnow that motif frequencies is also a nother solution. I have read in a paper that using frequency measure of motifs we can cluster genes. how can i use motif to cluster genes.
Can anyone tell me how to find motif frequencies for a geven gene.
for ex: how to find frequency motif for gene STU2 (from yeast genome)

Thanks a lot in advance,
Asanka.

ljxue · 07-17-2009, 04:24 AM

Firstly, a list of motifs should be obtained from some databases containing transcription factor binding site. Or you can get the motifs from your data using tools such as MEME,
Then map the elements onto your sequences using Patscan and so on.
Then summarize the number of sites.

asankaf · 07-17-2009, 07:53 PM

thanks a lot for your suggestions.
here I only know the gene name. how can I find a sequence for a given gene.
to find motif ,what sequence we use? DNA(in terms of A,T,C,G) or PROTIEN?

ljxue · 07-17-2009, 09:58 PM

I do not work on yeast, you can try the page
http://www.yeastgenome.org/cgi-bin/seqTools

Mostly,regulatin motifs refers to the cis-elements of the gene promoters.
The method I said it not for green hand.You can ask others good at
bioinformatics to help you to deal with your data.

If you want to cluster genes using the seqences of CDS,cDNA, or protein
you can simplely use MEGA. Your can also find these sequences
in http://www.yeastgenome.org

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07-17-2009, 01:19 AM	#1
asankaf Member Location: clayton Join Date: Jan 2009 Posts: 10	gene clustering using motif Hi, I am new to molecular biology and I am going to cluster yeast gene using several data sources. I know that gene can be clustered using gene expression data and using other alternatives. I klnow that motif frequencies is also a nother solution. I have read in a paper that using frequency measure of motifs we can cluster genes. how can i use motif to cluster genes. Can anyone tell me how to find motif frequencies for a geven gene. for ex: how to find frequency motif for gene STU2 (from yeast genome) Thanks a lot in advance, Asanka.

07-17-2009, 09:58 PM	#4
ljxue Junior Member Location: China Join Date: Jul 2009 Posts: 4	I do not work on yeast, you can try the page http://www.yeastgenome.org/cgi-bin/seqTools Mostly,regulatin motifs refers to the cis-elements of the gene promoters. The method I said it not for green hand.You can ask others good at bioinformatics to help you to deal with your data. If you want to cluster genes using the seqences of CDS,cDNA, or protein you can simplely use MEGA. Your can also find these sequences in http://www.yeastgenome.org Last edited by ljxue; 07-17-2009 at 10:12 PM.

07-17-2009, 04:24 AM	#2
ljxue Junior Member Location: China Join Date: Jul 2009 Posts: 4	Firstly, a list of motifs should be obtained from some databases containing transcription factor binding site. Or you can get the motifs from your data using tools such as MEME, Then map the elements onto your sequences using Patscan and so on. Then summarize the number of sites.

07-17-2009, 07:53 PM	#3
asankaf Member Location: clayton Join Date: Jan 2009 Posts: 10	thanks a lot for your suggestions. here I only know the gene name. how can I find a sequence for a given gene. to find motif ,what sequence we use? DNA(in terms of A,T,C,G) or PROTIEN?