Dear UCSC Genome Bioinformatics Group, Can you please advise me on my previous query? I am pasting the same below for your convenience: 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 ________________________________ From: Regalla, Kumarswamy Sent: Mon 05.12.2011 10:02 To: [email protected] Subject: FW: [Genome] LncRNAs hosting miRNAs 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 at [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
