Hi Niyati, Using the Table Browser, you can create custom tracks of the upstream and downstream regions around the genes of your gene track of interest (e.g. UCSC Genes). Then, using the Table Browser again, intersect each custom track with the Placental Mammal Conserved Elements using the Table Browser. For more information about the Conserved Elements, see "Conserved Elements" in the Methods section of the Conservation track description: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way.
To create your custom tracks, click on "Tables" on the blue bar on the top of the main page, select the hg19 human assembly and select your gene track of interest by selecting the appropriate group, track and table. Set the "output format" to "custom track." Click "get output." Enter a name and description for your custom track (such as " name=upstreamRegions" and "description=upstream from UCSC Genes"), select "Upstream by," and enter the number of upstream bases you want in the adjacent field. Click "get custom track in table browser." Repeat this for the downstream regions except name appropriately and select "Downstream by" and enter the number of downstream bases in the adjacent field. Now you should have two custom tracks, one with upstream regions and one with downstream regions. Next, intersect each of your custom tracks with the Placental Mammal Conserved Elements using the Table Browser. Here is information on the Table Browser intersection feature: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection I hope this information is helpful. Katrina Learned UCSC Genome Bioinformatics Group [email protected] wrote, On 10/17/2010 5:40 AM: > Hello, I am a students working on a project which needs to find the conserved > regions upstream and downstream of a gene in mammals. Please let me know how > to do that using mamamlian conservation graph or if not that by any other > method? Thanks a lot,Niyati > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
