Hi again, Sohini, There is yet another track with lincRNA annotations: GENCODE Genes (the latest is V11). The GENCODE gene set contains high-quality manual annotations in addition to Ensembl automatic annotations. The track description is here:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV11 Similar to the Ensembl track, you can set up a "lincRNA" filter, this time using the wgEncodeGencodeAttrsV11 table, with either the geneType or transcriptType field. To see all of the possible values for those fields, select the GENCODE Genes V11 track in the Table Browser, and hit "describe table schema." Scroll down to "Connected Tables and Joining Fields" and select the wgEncodeGencodeAttrsV11 table, then click on the "values" links in the info column on the resulting page. I hope this is helpful! If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 5/10/12 3:35 PM, Brooke Rhead wrote: > 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
