Hi Daniel, It looks like you have used the correct ENCODE tracks for your analysis, but we are unable to comment on the method you have used. If you need additional information on how to use the Table Browser, please see: http://genome.ucsc.edu/cgi-bin/hgTables#Help, or feel free to search the Genome mailing list archives by visiting our home page and clicking on "Contact Us" (http://genome.ucsc.edu/contacts.html).
Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 7/1/2011 4:16 PM, Daniel Diniz wrote: > Hello all, > > I need to answer some reviews questions and I'm trying to use some encode > data. > > I have a chip-seq data for one transcription factor (TF) in H1 ES cells. Now > I > need to prove the reviewers that this TF doesn't bind to regions with DNA > methylation and bind preferentially to regions without a nucleosome. What I > did > was: > > Load my Chip-seq data as a bed file into the genome browser. In the table > option, It has in the summary/statistic a item count of 29,740. > > In the table option, load the group: regulation, track: HAIB Methyl-seq, > table: > H1-hESC1 (wgEncodeHudsonalphaMethylSeqRegionsRep1H1hesc) > > Then, I used the filter option: score > 10 (to get the regions methylated). > This > gave me in the summary/statistic a item count of 42,263. > > Next I created an intersection marking only the option that hane any > intersection with my TF track: All > wgEncodeHudsonalphaMethylSeqRegionsRep1H1hesc > records that have any overlap with User Track > > > This gave a item count of only 34. Proving they are mutually exclusive. > > I did the same, using my TF track or the Methyl-seq track from encode against > the track UW DNAseI HS (wgEncodeUwDnaseSeqPeaksRep1H1es) (I didn't set any > threshold in the filter). > > Finally, I created a venn diagram showing the item count of the three groups > and > their intersections, proving my TF doesn't bind to methylated DNA and mostly > bindind to DNAseI hipersensitive regions. As expected it also shows that > DNAseI > HS and DNA methylation are mutually exclusive. > > Do you guys think I did it riqht? Any suggestion? > > Thanks! > > Daniel > > > > > > > ________________________________ > De: "[email protected]" <[email protected]> > Para: [email protected] > Enviadas: Sexta-feira, 1 de Julho de 2011 15:30:49 > Assunto: confirm 9a413e59c4712f1f3a198516e96c3e1d5923f021 > > Mailing list subscription confirmation notice for mailing list Genome > > We have received a request from 128.125.191.14 for subscription of > your email address, "[email protected]", to the > [email protected] mailing list. To confirm that you want to be > added to this mailing list, simply reply to this message, keeping the > Subject: header intact. Or visit this web page: > > > https://lists.soe.ucsc.edu/mailman/confirm/genome/9a413e59c4712f1f3a198516e96c3e1d5923f021 > > > > Or include the following line -- and only the following line -- in a > message to [email protected]: > > confirm 9a413e59c4712f1f3a198516e96c3e1d5923f021 > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > [email protected]. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
