Genes with CpG islands...database?

[CrowSan]

Hi I am looking for a database/list with human genes that are associated with CpG islands. Ideally the database would be searchable (i.e. I type in a gene and it tells me if there is a known CpG island associated with it). I have tried a quick "google" but most of the results are for databases that either identify CpG islands in a strectch of DNA or are for searching within CpG islands for promoter sequences.
Thanks in advance
CrSn

[Abhijeet Bakre]

Hi I am looking for a database/list with human genes that are associated with CpG islands. Ideally the database would be searchable (i.e. I type in a gene and it tells me if there is a known CpG island associated with it). I have tried a quick "google" but most of the results are for databases that either identify CpG islands in a strectch of DNA or are for searching within CpG islands for promoter sequences.
Thanks in advance
CrSn

What do you exactly mean by associated with Cpg islands? in the vicinity of CpG islands, have CpG islands on them or other? Try looking up NCBI gene and that may have information on it? Alternately you may want to download sequences of genes of your interest and get them analyzed by a tool as such you refer above.
AB

[CrowSan]

Thanks for the reply. In the end I used USCS's "Genome" programme. In the advanced search area you can "tick" a section if you want it to shown known CpG rich areas/islands near to an inputted gene. Thanks anyway
CrSn

[morkfromork]

Hi Crowsan,
If you want to create a list of all genes with CpG islands you can use UCSC GB table browser to create an intersect of Refseq genes and CpG islands (might be necessary to extend the length of CpG islands in case they are a little upstream of the first exon and don't completely overlap). Another way would be to use something like the R/Bioconductor package ChIPpeakAnno and annotate a BED file of CpG islands (again you could get this from UCSC GB) to the nearest gene or TSS.

But I think if you just want to look at a relatively small set of genes just looking at the genome browser with the CpG island track turned on is probably the fastest way. But if you decide you want to make a genome wide list of CpG island promoters and you get stuck with the software give me a shout and I will try to help you out.