Hi, I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinder of my choice I'm using the Galaxy tool from the UCSC browser to manipulate my intervals. What I have is a file in .BED format with the chromosome number, Start, End of the position and then I fetch the closest features and up to this moment everything is perfect but now that I have the positions of the nearest features to my putative binding sites I would like to get the gene symbol, description y GO for each one of them in a sort of table so as I can analyze it later on and make relationships. Is there a direct tool between Galaxy and a Gene ontology database? Any help about this topic will be appreciated. Thank you in advance.
Oscar:
If you are fetching UCSC genes closest to your peaks, you will have their accession numbers. To go from accession numbers to gene symbols you will need to grab kgXref table from UCSC and then join results of "Find closest feature" with kgXref using "Join, Subtract and Group -> Join" tool. I am not quite sure how to get to GO categories for these gene symbols from there.
Let me know if you have problems.
Thanks,
anton galaxy team
On Dec 8, 2009, at 5:43 PM, Oscar V Camacho wrote:
Hi, I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinder of my choice I'm using the Galaxy tool from the UCSC browser to manipulate my intervals. What I have is a file in .BED format with the chromosome number, Start, End of the position and then I fetch the closest features and up to this moment everything is perfect but now that I have the positions of the nearest features to my putative binding sites I would like to get the gene symbol, description y GO for each one of them in a sort of table so as I can analyze it later on and make relationships. Is there a direct tool between Galaxy and a Gene ontology database? Any help about this topic will be appreciated. Thank you in advance. _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
On Wed, Dec 9, 2009 at 10:35 AM, Anton Nekrutenko anton@bx.psu.edu wrote:
Oscar:
If you are fetching UCSC genes closest to your peaks, you will have their accession numbers. To go from accession numbers to gene symbols you will need to grab kgXref table from UCSC and then join results of "Find closest feature" with kgXref using "Join, Subtract and Group -> Join" tool. I am not quite sure how to get to GO categories for these gene symbols from there.
Just a little note here--while people often say they want GO categories for each gene, what they usually actually want is to compute the enrichment of a set of GO terms relative to what would be expected by random chance given a set of genes. If the latter is what the original intent was, I would suggest stopping at the Gene Symbol level and then use any of a couple of dozen online and standalone tools for GO enrichment/GSEA analysis with input as Gene Symbol.
Sean
On Dec 8, 2009, at 5:43 PM, Oscar V Camacho wrote:
Hi, I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinder of my choice I'm using the Galaxy tool from the UCSC browser to manipulate my intervals. What I have is a file in .BED format with the chromosome number, Start, End of the position and then I fetch the closest features and up to this moment everything is perfect but now that I have the positions of the nearest features to my putative binding sites I would like to get the gene symbol, description y GO for each one of them in a sort of table so as I can analyze it later on and make relationships. Is there a direct tool between Galaxy and a Gene ontology database? Any help about this topic will be appreciated. Thank you in advance. _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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Anton Nekrutenko -
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Sean Davis