software for CpG island prediction for a list of genes - (Nov/01/2007 )
Hi,
I have an output file from an microarray experiment with a long list of interesting genes. I would like to find which of the genes that have a CpG island. Since there are so many genes I was hoping of not having to check them gene by gene. Does anyone know if there is some kind of sofware for CpG island prediction that you can use to search a list of gene names?
Thanks
UCSC Genome and Table broswers are your friend :-)
Genome Browser
Nick
I asked the same question about two weeks back. I hope the link works: http://www.protocol-online.org/forums/inde...showtopic=31404
I did find it hard to understand at first, and I am still getting my head around it. Here are some instructions I have:
To make a custom track, do the following: (This creates a list of genes with CpG islands)
clade: Vertebrate, genome: Human, assembly: Mar. 2006
group: Expression and Regulation, track: CpG Islands
table: cpgIslandExt, region: genome
output format: Custom Track
click: "Get output"
click: "Get custom track in table browser"
Now, in table browser, enter these settings: (This is where you enter your list of genes to match up with the list of genes with CpG islands)
clade: Vertebrate, genome: Human, assembly: Mar. 2006
group: Genes and Gene Prediction Tracks, track: RefSeq Genes
table: refGene
region: genome
Identifiers: (paste in the accession numbers of the genes you want to look up. Get rid of decimal places from the end of accession numbers, this can be easily done in excel)
Intersection: On the intersection menu page, change to:
group: Custom Tracks
track: CpG Islands Custom Track (the default name was cpgIslandExt)
table: CpGIslandExt (ct_cpgIslandExt) or whatever you named it.
press submit
output format: BED
click: "get output"
The output file will have a big list of columns, and you can interpret what these mean from the help file on the UCSC website at http://genome.ucsc.edu/FAQ/FAQformat#format1
Good luck,
Dave
Thanks a lot! That really helped me!