Hello Bogdan,
To get this data you will need to cross reference two of the tables from
our Gencode Genes track with the subset of items in our RepeatMasker
track that are tagged as Alu elements. You can do this using a couple
iterations of queries on our Table Browser
(http://genome.ucsc.edu/cgi-bin/hgTables) as follows:
Round 1 (creating a custom track of Gencode items tagged as lincRNAs):
group:Genes and Gene Prediction Tracks
track: Gencode Genes
table: wgEncodeGencodeAutoV4
region: genome
filter: click "create"
then scroll down to the "Linked Tables" section and select the
'wgEncodeGencodeClassesV4' table and click "Allow Filtering Using Fields
in Checked Tables"
This should bring up a new section:
"hg19.wgEncodeGencodeClassesV4 based filters"
In this section set:
transcriptType does match lincRNA
Then click "submit".
Now back in the main Table Browser menu select:
output format: "custom track"
Once you click on "get output" this will take you to a menu where you
can specify how to receive your custom track and you should pick "get
custom track in table browser".
Round 2 (intersecting your custom track with Alu* elements in the
RepeatMasker track):
Back in the table browser you should now select the following:
group: Variation and Repeats
track: RepeatMasker
table: rmsk
region: genome
filter: click "create"
in the "Filter on Fields from hg19.rmsk" section set:
repFamily does match Alu*
and click "submit"
Now back in the main Table Browser menu:
intersection: click "create"
and in the intersection menu select your custom track:
group: Custom Tracks
track: (whatever you called the track from Round 1 - if you didn't
change the default this will be something like
"ct_tbwgEncodeGencodeAutoV4")
table: this name will be similar
then click submit and in the main menu select your output format of
choice and click "get output".
Note that the lincRNAs in the Gencode track are predicted by Ensembl and
they may not therefore be experimentally verified. There are some other
ncRNA resources out there that you could try. http://www.ncrna.org is
one and from there, there is a link to fRNAdb which has ncRNA
annotations - they have an implementation of the Genome Browser.
Best regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
On 03/02/11 13:30, Bogdan Tanasa wrote:
> Dear all,
>
> please could you let me know the way you recommend to identify
> mRNAs(lincRNAs) with ALU elements in 3' UTR ... thanks,
>
>
> Bogdan
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
