Hi Kumar, I've tried intersecting lincRNAs with a couple different tracks that contain miRNA data, and do get more than 1 result, but still not that many. I would suggest looking at the article you mention and see if there are some specific examples given and then l ook to see if we have any tracks that contain the lincRNA or the miRNA.
You can list LncRNAs using the table browser: http://genome.ucsc.edu/cgi-bin/hgTables 1. Select genome/assembly 2. Group: Gene and gene prediction tracks Track: lincRNA RNA-Seq reads Table: (choose table corresponding to tissue of interest) Region: genome Output format: all friends from selected table (if you want to download the data, provide a file name) 3. "get output" Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 12/5/11 1:02 AM, [email protected] wrote: > Dear Brooke Rhead, > Dear UCSC Genome Bioinformatics Group, > > Many thanks for your prompt advise, but in this way I am also able to > see only one hit (that is miR-675, on chr 11) that you mentioned. I read > in a recent Cell paper that about 8% of miRs are hosted by LncRNA genes. > Is there any way to use less stringent filters? > > Can you also please advise me on if it is possible to list out LncRNAs > that are specifically expressed in a particular tissue like heart? > > Best regards > > Kumar > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Saturday, December 03, 2011 2:35 AM > To: Regalla, Kumarswamy > Cc:[email protected] > Subject: Re: [Genome] LncRNAs hosting miRNAs > > Hi Kumarswamy, > > You could go about looking for microRNAs within lncRNAs by identifying > tracks that contain the RNAs and then using the Table Browser to > intersect them. > > To find relevant tracks, use the "track search" button (just beneath the > main graphic in the Genome Browser), or browse the tracks in the "Genes > and Gene Prediction Tracks" section. (There is a track called > "sno/miRNA" and another called "lincRNAs...," but there may be others.) > > If you have not used the Table Browser before, there is a good > introduction to it here: > http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 > also see the user's guide: > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html > > I tried doing an intersection by selecting the "linkRNA Transcripts" > track in the Table Browser and using the "intersection: create" button > to create a base-pair-wise intersection with the sno/miRNA track. This > found one region of intersection, at chr11:2,017,989-2,018,061 (using > the GRCh37/hg19 assembly). > > I hope this helps you get started. If you have further questions, > please contact us again [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > > On 12/2/11 8:04 AM,[email protected] wrote: >> Dear USCC Genome people, >> >> I am a post-doc at Hannover Medical School. Many protein coding genes >> host microRNAs, mostly in their intronic regions. Can you please >> advise me if there is a way to know what are the microRNAs that are >> hosted by LncRNA genes? >> >> Best regards Kumarswamy >> _______________________________________________ Genome maillist - >> [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
