Hi Karmella, I'm glad you are finding the Genome Browser useful. I just sent a response to Carly's email with more or less the same answers:
> 1. Is there a resource where we can read more details about the "Score" for histone methylation signal? Would this be in the Sabo et al 2004 paper? The "describe table schema" button with the table selected in the Table Browser will get you a brief description of the score and a range of values. If that doesn't elucidate the meaning of the score, I suggest checking out the paper or contacting the person listed as the contact in the Credits section of the track description. > 2. Once we generate a list of "highly methylation score" regions, > can the filters and/or table intersect tools be used to retrieve the methylated regions that are located within –500 and +500 base pairs of every annotated transcription start site? Yes, but the Table Browser results will only have rows from the promoter regions table or from the high methylation score table, but not both. (The Table Browser won't do a join of the tables.) This might be fine for your purposes, or you might want to use Galaxy (http://main.g2.bx.psu.edu/), which will do joins. Also, I should point out that it is possible to use any gene set in the Genome Browser to determine transcription start sites . . . we suggested UCSC Genes and the knownCanonical table because it contains a representative transcript for each cluster of transcripts. Alternatively, there is a track that consists of only annotated transcription start sites: SwitchGear TSS. This track was lifted from the hg17 assembly and comes with some caveats: http://genome.ucsc.edu/goldenPath/help/hg18ToHg19LiftOver.html Good luck with your project! Let us know if you have further questions on these instructions. -- Brooke Rhead UCSC Genome Bioinformatics Group On 2/7/12 10:14 AM, Karmella Haynes wrote: > Hello, > > I'm Carly's mentor. I'd just like to follow up by thanking you for > all of your assistance with browsing the data hosted on your website. It's an invaluable resource. Your tips have allowed us to make a lot of progress so far. > > We are curious about a couple of specific things… > > 1. Is there a resource where we can read more details about the "Score" for histone methylation signal? Would this be in the Sabo et al 2004 paper? > 2. Once we generate a list of "highly methylation score" regions, > can the filters and/or table intersect tools be used to retrieve the methylated regions that are located within –500 and +500 base pairs of every annotated transcription start site? > > Once we get these questions squared away, we will continue working > on our project with the help of bioinformatics colleagues here at ASU. Thanks again for helping us to become more familiar with the ENCODE data hosted by the UCSC Genome Browser site. > > Best, > ---Karmella > > -- > Karmella A. Haynes, Ph.D. > Assistant Professor > School of Biological and Health Systems Engineering > Arizona State University > 501 E. Tyler Mall, ECG 346 > Tempe, AZ 85287 > E-mail: [email protected] > Website: haynes.lab.asu.edu > > > From: Carly Hom<[email protected]<mailto:[email protected]>> > Date: Sat, 4 Feb 2012 02:41:59 -0700 > To: > "[email protected]<mailto:[email protected]>"<[email protected]<mailto:[email protected]>> > Cc: Karmella Haynes<[email protected]<mailto:[email protected]>> > Subject: Question: Table Browser Filtering > > 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 lin es. 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). I f 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 > availab le 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
