[Genome] Human lncRNA list

[Hani Choudhry]

Dear UCSC Genome,

I am trying to download database (Name, chromosome location) of human long non coding RNA (=> 200 bps), using the instruction sent by your team. Thanks for sending the instruction, it was useful.

But I realised that several long non coding RNA (NR_) have same name as protein coding RNA (NM_), for examples: AMT, GYS1, LDHA.

I am wandering, if there is any filter to obtain all the NR_ which have no NM_ ? In other words, to get list of long non coding RNAs which have no protein coding transcripts?

Thanks for your attention and look forward to your reply.

Regards,
Hani

..........................................................................
Hani Choudhry,
Genomic Research Lab
Wellcome Trust Centre of Human Genetics
Nuffield Dept of Clinical Medicine
University of Oxford
Oxford- UK
Lab tel: +44-1865287519
Mobile: +44-7771219664
Email: hani.c...@ndm.ox.ac.uk
________________________________________
From: Katrina Learned [kat...@soe.ucsc.edu]
Sent: 28 March 2011 20:24
To: Hani Choudhry
Cc: gen...@soe.ucsc.edu
Subject: Re: [Genome] Human lncRNA list

Hi Hani,

You can further filter the list you retrieved via the table browser by
adding another parameter to your filter:

filter: click 'create' then in the 'name DOES match' field type: NR_*
and then scroll down to the 'AND Free-form query:' and
type: txEnd - txStart >=200

This will provide you with data for all non-coding RNAs that are greater
than or equal to 200 bp. You can change the "200" to whatever base-pair
number you consider to be the minimum base-pair length of long
non-coding RNAs.

To obtain the sequence for each long non-coding RNA, do the same query
(including the updated filter information I've provided above) but for
output select 'sequence.' After clicking 'get output' select 'mRNA' and
click submit.

I hope this information is helpful! Please don't hesitate to contact the
mail list again if you have any further questions.

Katrina Learned
UCSC Genome Bioinformatics Group


Hani Choudhry wrote, On 03/25/11 05:49:
> Dear UCSC,
> Thanks for your reply. The instructions were very helpful to download all non coding RNAs.
>
> However, I only want list of long non coding RNAs (name, Chromosomal location, strand and sequences) based on �NCBI 37/ Hg19�
>
> Or how can I isolate long non coding RNAs from all non coding RNA list?!
>
> This information will be very useful and I will be greatly appreciated your help.
>
> Thanks for your attention and look forward to your reply soon.
>
> Sincerely,
> Hani Choudhry
> ________________________________________
> From: Luvina Guruvadoo [luv...@soe.ucsc.edu]
> Sent: 17 March 2011 19:52
> To: Hani Choudhry
> Cc: gen...@soe.ucsc.edu
> Subject: Re: [Genome-mirror] Human lncRNA list
>
> Hi Hani,
>
> The information you are requesting can be retrieved using the Table
> Browser. Click on "Tables" on the blue bar on the top of the main page
> and make the following selections:
>
> clade: Mammal
> genome: Human
> assembly: hg19
> group: Genes and Gene Prediction Tracks
> track: RefSeqGenes
> table: refGene
> region: genome
> filter: click 'create' then in the 'name DOES match' field type: NR_*
> output format: select fields from primary and related tables
> output file: if you would rather have the results saved to a file
> instead of displaying in the browser window, enter the name you would
> like the output file to have, otherwise, leave blank
> file type returned: plain text
>
> Click "get output". From here, select the following: name, chrom,
> strand. Click "get output". This will provide a list of non-coding RNA
> names, positions, and strands. To retrieve sequences, go back to the
> table browser and set the same settings, except set 'output format' to
> 'sequence'.
>
> I hope this helps. Feel free to contact us again at gen...@soe.ucsc.edu
> if you have further questions.
>
> ---
> Luvina Guruvadoo
> UCSC Genome Bioinformatics Group
>
>
> Hani Choudhry wrote:
>
>> Dear UCSC,
>> It is my pleasure to contact you. I am a PhD student, working on non-coding RNA regulation in cancer, in particular long non-coding RNA.
>> I am wondering if you can help in downloading all Human long non-coding RNA list (name, Chromosomal location, strand and sequences) based on �NCBI 37/ Hg19� from your website?!
>> This information will be very useful for my PhD project and I will be greatly appreciated your help.
>> Thanks for your attention and look forward to your reply soon.
>> Sincerely,
>> Hani
>>
>> ..........................................................................
>>
>> Hani Choudhry,
>>
>> Genomic Research Lab
>>
>> Wellcome Trust Centre of Human Genetics
>>
>> Nuffield Dept of Clinical Medicine
>>
>> University of Oxford
>>
>> Oxford- UK
>>
>> Lab tel: +44-1865287519
>>
>> Mobile: +44-7771219664
>>
>> Email: hani.c...@ndm.ox.ac.uk<mailto:hani.c...@ndm.ox.ac.uk>
>> _______________________________________________
>> Genome-mirror mailing list
>> Genome...@soe.ucsc.edu
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror
>>
>>
> _______________________________________________
> Genome maillist - Gen...@soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist - Gen...@soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>

[Steve Heitner]

Hello, Hani.

First, I want to clarify that even though some of the non-coding RNAs (NR_*)
and protein-coding RNAs (NM_*) may share the same gene name, all of the NR_*
results are for non-coding RNAs. If all you want is non-coding RNAs in your
results, you should not need to filter your results any further.

If you do not want any NR_* results that share a gene name with any of the
NM_* results, our Table Browser does not have the capability to filter the
results based on your criteria. There is no simple way to achieve what
you're asking, but it could be accomplished by writing a custom script.
Unfortunately, we cannot provide you with assistance with that as it is
outside the scope of this forum.

Please contact us again at gen...@soe.ucsc.edu if you have any further
questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

location, strand and sequences) based on "NCBI 37/ Hg19"

RNA list (name, Chromosomal location, strand and sequences) based on "NCBI
37/ Hg19" from your website?!