Hello, I received a response from you receiving instruction on how to filter the browser according to these instructions:
Hi my name is Carly Hom and I am an undergraduate student researcher at Arizona State University working with Dr. Karmella Haynes. In my current lab I am using Synthetic Biology and Bioinformatics toinvestigate reliable and predictable reactivation of dormant genes that can help treat cancer and enable tissue re-growth. By determining which silenced genes will switch to an active state in osteosarcoma cells, with the presence of the synthetic transcription factor PC-TF, my work will establish a comprehensive method for predicting the effect of rationally designed protein-based drugs. Pc-TF, a synthetic transcription factor developed by Dr. Haynes, regulates cell states by binding the repressive trimethyl-histone H3 lysine 27 signal (H3K27me3) and switching silenced genes to an active state in osteosarcoma cells. Since a comprehensive ChIP map is not available for osteosarcoma, I will be identifying genes associated with H3K27me3 in liver (HepG2) and fibroblast (BJ) cell lines. Overall, I will need to collect about 1000 genes from the ENCODE database that show a significant enough H3K27me3 signal at the promoter of the gene. I have already figured out how to project only information from the HepG2 and BJ cell lines in relation to H3K27me3, but by just clicking to move through the cell line to find genes will take entirely too long and can cause me to miss important genes. At the request of Dr. Haynes I am asking if ENCODE has some sort of filter program that will provide a list of genes where the promoter site shows a high level of the H3K27me3 histone methylation. I will need it to be able to find the beginning of the gene's promoter on the UCSC Genome Browser and then show about 500bps to the left and 500bps to the right of the promoter . Ultimately, I want to be able to navigate through the genes in this cell line that show a significant enough H3K27me3 signal at the promoter (everything else with a low H3K27me3 signal I do not care about). If you could get back to me on whether this is even possible to do within the Genome Browser, and if yes, how I would be able to do this that would be great. Thank you! After a couple of emails back and forth this was the best response we received: Hello, Karmella. To expand upon Luvina's instructions, to create the filter, perform the following steps in the Table Browser: 1. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Genes and Gene Prediction Tracks Track: UCSC Genes Table: knownCanonical 2. Next to "filter", click the "create" button 3. In the "Linked Tables" section, scroll down and check the hg19.knownGene checkbox 4. Scroll to the bottom of the page and click the "Allow Filtering Using Fields in Checked Tables" button 5. In the "hg19.knownGene based filters" section, the third line should read "strand does match +" 6. Click the "submit" button Also note that these tables: wgEncodeUwHistoneHepg2H3k27me3StdPkRep1 wgEncodeUwHistoneHepg2H3k27me3StdPkRep2 wgEncodeUwHistoneBjH3k27me3StdPkRep1 wgEncodeUwHistoneBjH3k27me3StdPkRep2 contain the methylation scores for H3k27me3 in Hepg and Bj cell lines as calculated according to the process outlined in the UW Histone track description here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeUwHistone and in the reference contained therein. You may also be interested in these additional tables: wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep1 wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep2 wgEncodeUwHistoneBjH3k27me3StdHotspotsRep1 wgEncodeUwHistoneBjH3k27me3StdHotspotsRep2 which also contain methylation hotspot data. You can read more about both sets of tables in the aforementioned description. Please be aware that the encode tables contain all the methylation scores, not just the high scores. If you're only interested in the high methylation scores, you'll need to filter the encode tables similar to my above example: 1. Select the following options: Clade: Mammal Genome: Human Assembly: Feb. 2009 (GRCh37/hg19) Group: Regulation Track: UW Histone Table: select the appropriate tables 2. Next to "filter", click the "create" button 3. Edit the "score" line so that it contains the values you are interested in such as "score is >= 500" 4. Click the "submit" button These instructions helped me out a lot, but I still need couple more things to be done. If certain things are not possible let me know. I am aware that I can check the boxes chrom, chromeSTART, and chromeEND and then copy and paste that into the Genome Browser. Is it possible for the tables to provide the location of the promoter (+/- 500bps to the left and right of that region) instead of a being thrown onto a random area of the gene? Also, how exactly is the histone methylation score measured? I want to be able to select a specific score range (ex: >= 500), but I am unsure of what to qualify as a significant enough of a signal since I do not know what the score is being measured relative to and what the top score possible is. Lastly, is there a way to add the gene name to the table output? It makes it a lot easier than having to determine the gene names when some genes are very close to each other and have an area of overlap. I know that the gene name check box is available in the group knownCANONICAL, but I can't seem to find it when I am in the Regulation group with the 'selected fields from primary and related tables' output format. If you could get back to me on these items that would be great. Thank you! - Carly -- Caroline Hom Tempe, AZ Ph: 602-315-5728 Arizona State University Ira A. Fulton Schools of Engineering Biomedical Engineering _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
