Hi Ahmed, The steps you followed took your original list of 2040 genes and checked them for overlap with CpG islands. The results of these steps is the subset of genes from your original list that overlap with CpG islands (genes from your list that did not overlap at all with CpG islands were excluded from your results).
The reason your results contain more genes than your original list is that many genes have multiple transcripts. So, some of the genes on your original list have multiple transcript that overlap with a CpG islands. To get the gene name from the accession number you can use the table browser again. Select: group: Genes and Gene Prediction Tracks track: Ref Seq Genes table: refGene region: genome identifiers (names/accessions): paste or upload the accession numbers output format: selected fields from primary and related tables Click 'get output'. Scroll to the bottom of the next page and under "Linked Tables" select hg19.refFlat; click 'Allow Selection From Checked Tables.' From hg19.refGene select 'name' and from hg19.reFlat select 'geneName.' Then click 'get output.' Your results will be your list of accession numbers with their corresponding gene names. I hope this information is helpful. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/4/11 8:22 PM, Ahmed Khamas wrote: > Dear respected, > Thank you very much for your prompt reply. From your valuable answer I could > understand that the steps I'd done will give me a list for genes that have > CpGi only. There are 2420 genes in my CpGi list (which should be the same in > your list!), but I need to know only my list of genes (2040 genes) those > whom I paste their names as Identifiers in the table browser steps! > According to your answer this will mean that the 2040 genes (not all of them > but only those with CpGi) are part of the 2420 genes list, if so, can you > please let me know a simple way to have the genes name back from the > accession number in the CpGi list! > > With my Best regards, > A. Khamas > M.B.Ch.B, PhD candidate > Surgical Oncology Department > Medical Faculty, Tokyo Medical and Dental University > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
