Hi Mahesh, Yes, you can definitely do this work with the Genome Browser, by first uploading your data as a Custom Track, and then using the Table Browser to intersect a gene track with your custom track. A quick online tutorial for using custom tracks and the table browser is here: http://www.openhelix.com//cgi/tutorialInfo.cgi?id=28 (click on the "Launch" button for the online tutorial)
Your data looks like it is very close to BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 Specifically, to get your data into BED format, you will need to move the "CpG Id" field to the 4th position instead of the 1st (so it will appear in the "name" field in BED format), remove the "Length" field and subtract 1 from each of the Start coordinates (see this FAQ: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1). You will also need to remove the space in the name field (change "CpG: 125" to "CpG:125" so that it is not interpreted as two different fields. Once you have your custom track uploaded, you can use it to create an intersection with a gene track in the Table Browser. To do this, go to http://genome.ucsc.edu/cgi-bin/hgTables and select "Genes and Gene Prediction Tracks" from the group drop-down. The most appropriate gene set to use for this is up to you, but you can get more information on each one by hitting the "describe table schema" button. Next, make sure region is set to "genome", and hit the "intersection: create" button. On the following page, you will be able to select your custom track from the drop-down menus, and you will be given options to select how much overlap you want to require. You will end up with a list of genes from the track you selected. If you would like to keep information from both the gene track and your custom track in the output, you may want to use Galaxy instead: http://main.g2.bx.psu.edu/ Galaxy works in conjunction with the Table Browser and has extended options for joining tables and manipulating text. I hope this is helpful. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/08/10 13:12, Mohan, Mahesh wrote: > Hi > > A private company has designed a CpG island microarray for my > personal use. The array consists of a total of 23985 unique CpG regions. They have provided me info as shown in the table below: > CpG Id Chromosome Start End Length > CpG: 125 chr1 13451 15132 1682 > > There are a total of 23985 such unique regions identified from the Rhesus macaque genome assembly. My immediate goal is to identify the genes that incorporate these CpG regions/islands. Is there is a way that I could upload the information shown above for all 23985 CpGs on the UCSC genome browser and then get an output file that would show the names of the rhesus specific genes that contain these CpG islands. > > Your help is greatly appreciated. > > Thanks > > Mahesh > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
