Hi Sohini, There are a few ways you could go about getting long noncoding RNAs from the Genome Browser.
There is a relatively new (from October, 2011) "lincRNAs" track in the Genome Browser: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=lincRNAs The data from this track can be downloaded from the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables; find the track in the "Genes and Gene Prediction" group) or the annotations portion of the downloads server: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ Another way would be to use the Table Browser to get long non-coding genes out of the RefSeq Genes track. See this previously-answered question for instructions: https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025470.html Yet another way would be to use the Ensembl Genes track. The "ensemblSource" table has the following gene classifications: +--------------------------+ | source | +--------------------------+ | protein_coding | | snRNA | | snoRNA | | miRNA | | rRNA | | pseudogene | | misc_RNA | | antisense | | lincRNA | | processed_transcript | | Mt_tRNA_pseudogene | | sense_intronic | | tRNA_pseudogene | | scRNA_pseudogene | | snoRNA_pseudogene | | ambiguous_orf | | polymorphic_pseudogene | | rRNA_pseudogene | | retained_intron | | miRNA_pseudogene | | snRNA_pseudogene | | non_coding | | 3prime_overlapping_ncrna | | ncrna_host | | misc_RNA_pseudogene | | TR_V_gene | | TR_V_pseudogene | | TR_D_gene | | TR_J_gene | | TR_C_gene | | TR_J_pseudogene | | sense_overlapping | | IG_C_gene | | IG_C_pseudogene | | IG_J_gene | | IG_J_pseudogene | | IG_D_gene | | IG_V_gene | | IG_V_pseudogene | | Mt_tRNA | | Mt_rRNA | +--------------------------+ 41 rows in set (0.14 sec) You can select either the ensGene table in the Table Browser, and then add a filter so that "source does match lincRNA" (or any of the other categories listed). If you are new to the Table Browser, I suggest looking at the online tutorial for it first: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 5/9/12 5:54 AM, sohini wrote: > > Hello, > I would like to know if a complete list of long noncoding RNAs or > specific > subtypes could be downloaded from UCSC and how to retrieve the data.Kindly > reply > soon. > Regards, > > -Sohini Chakraborty > CSIR-Junior Research Fellow > CoE in Bioinformatics > Bose Institute > DST, Govt. of India > > -- > Open WebMail Project (http://openwebmail.org) > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
