Hi Jessilyn, The UCSC Genes track would be of interest to you. Here is a link to that track description page for the UCSC Genes track in hg19:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr17&g=knownGene When in the hg19 genome browser you can search for the "klf4" gene by using the input box above the image and clicking "jump" To get the coordinates of the transcription and coding region start and end positions click on the gene in the image. This will take you to a gene details page. Then on the page you will see a link to "Table Schema". Click that and this will have the information that you are after. The description page should be able to answer your questions about how this track was generated. If you have multiple genes that you are interested in we recommend using the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) to extract the coordinates for the transcription and coding region start and end positions. To use the table browser select hg19 and then select the following: group: Genes and Gene Prediction Tracks track: (for this example we'll choose UCSC genes) table: knownGene region: genome identifiers (names/accessions): paste in the genes of interest like "KLF4" To get coordinates across the whole genome make sure you have region: genome selected. Then choose: output format: selected fields from primary and related tables This will take you to a menu where you can select which fields (i.e. gene name, coordinates, etc) you want to include in the output. To find other tracks of interest we recommend using our track search feature which can be accessed from gateway page: (http://genome.ucsc.edu/cgi-bin/hgGateway) and then clicking on "track search". This will help you find tracks that cover 'Transcription factor binding sites" which you can use to compare with your custom track. If you are interested in the promoter sequences, please see this FAQ: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download18 To compare human with mouse, we have a Placental Chain/Net Track which displays alignments of human to other genomes: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr9&g=placentalChainNet Hopefully this helps you get started. If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Jessilyn Dunn <[email protected]> Date: Tue, Mar 6, 2012 at 11:54 AM Subject: [Genome] viewing promoter regions for DNA methylation comparison To: [email protected] Hello, How can I view a gene promoter in the UCSC browser? Is there a track to view promoter regions and the gene coding region at the same time? Also, does the UCSC have a defined region for the promoter of each gene individually, or does it just give you a preset upstream region (such as 1,2,and 3kb upstream, but no defined region). I have custom tracks of DNA methylation data and I would like to see where this methylation is occurring in comparison to the transcriptional regulatory regions (Transcription factor binding sites, etc.). The gene I am specifically looking at is klf4. I am able to reference it to the nucleotide regions, but I cannot tell if the region in within the gene itself or within the promoter region. Additionally, it would be helpful if I could compare these regions between mouse and human genes at the same time. Any assistance would be greatly appreciated!! Thank you, Jessilyn -- Jessilyn Dunn Graduate Research Assistant, Jo Lab Dept. of Biomedical Engineering Georgia Institute of Technology & Emory 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
