How One Can Separate Noncoding From Coding Ucsc And Ensembl Transcripts

Question

[biorepine]

Dear biostars,

Do you know how one can separate noncoding from coding UCSC and ENSEMBL transcripts ? In general I use NR_* to identify noncoding and NM_* to identify protein coding genes in Refseq database.

Thanx in advance

[Pierre Lindenbaum]

what is your input ? a list of knownGene identifiers ? a list of ENSGxxxxxxx ?

[biorepine]

yes ENS* in case of ENSEMBL and ucsc.* in case of UCSC.

[Pierre Lindenbaum]

ucsc.* ? can you give one example please.

Answer 1

[Pierre Lindenbaum]

for the ucsc/knownGene, you can select the transcripts having cdsStart==cdsEnd

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select name,chrom,cdsStart,cdsEnd from knownGene where cdsStart=cdsEnd limit 10'
+------------+-------+----------+--------+
| name       | chrom | cdsStart | cdsEnd |
+------------+-------+----------+--------+
| uc001aaa.3 | chr1  |    11873 |  11873 |
| uc010nxr.1 | chr1  |    11873 |  11873 |
| uc009vis.3 | chr1  |    14361 |  14361 |
| uc009vit.3 | chr1  |    14361 |  14361 |
| uc009viu.3 | chr1  |    14361 |  14361 |
| uc001aae.4 | chr1  |    14361 |  14361 |
| uc001aah.4 | chr1  |    14361 |  14361 |
| uc009vir.3 | chr1  |    14361 |  14361 |
| uc009viq.3 | chr1  |    14361 |  14361 |
| uc001aac.4 | chr1  |    14361 |  14361 |
+------------+-------+----------+--------+

[biorepine]

So if I change cdsStart!=cdsEnd, does it print only coding genes ? Thanks

Answer 2

[Ashutosh Pandey]

You can download ENSEMBL annotation from Biomart (http://useast.ensembl.org/biomart/martview/) , you can select Gene Biotype information that will tell you if a given transcript is protein-coding or non-coding.

[biorepine]

Thanx but any idea regarding UCSC transcripts ?

[Emily]

You can input UCSC IDs into BioMart.

There's a help video on BioMart here:

[hbr721]

Using Ensembl biomart, is it possible to find gene biotype on the opposite(antisense) strands, especially if it is coding and non-coding.

[Emily]

I'm afraid I don't understand your question. Are you looking to find out if there's a gene on the opposite strand of your gene of interest and find out what its biotype is? If so, there isn't a way to do that using BioMart. That would be a job for the Perl API.

[hbr721]

I am sorry that my question was not clear. But still you got it right - yes I am indeed interesting in looking on the non coding genes on the opposite strand of my gene of interest. I will look into Perl API. Thanks again.

[Emily]

There's an online course here. http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop

[hbr721]

Great !!! thanks so much. Currently i am trying to see the reverse strand information from the Blat output, if i can't then i have to switch to perl api.

[biorepine]

I think hundreds of ENSEMBL lincRNAs annotations were wrong. (They should be intergenic and in principle they should not overlap with any known coding transcript irrespective of strand direction)

ex:

chr8    33998976    34060498    NM_001177589_Gm3985    0    -    chr8    33998977    34060498    lincRNA_ENSMUSG00000079070_ENSMUST00000132101_Gm3985    0    -
chr8    33998976    34060498    NM_001177589_Gm3985    0    -    chr8    34000947    34052954    lincRNA_ENSMUSG00000079070_ENSMUST00000180220_Gm3985    0    -
chr8    48265402    48437702    proteinCoding_ENSMUSG00000038143_8_Stox2    0    -    chr8    48379626    48531716    lincRNA_ENSMUSG00000097922_ENSMUST00000181417_AC102862.2    0    -

[Emily]

I'm afraid you've got that wrong. lincRNAs can be anywhere in the genome and can overlap coding genes in both directions.

See the wikipedia article on lincRNAs.

[biorepine]

Please see the wiki again.

Long intergenic non-coding RNAs (lincRNA) : "Intergenic" refers to long non-coding RNAs that are transcribed from non-coding DNA sequences between protein-coding genes"

[Emily]

Whoops yes. I googled lincRNA for a definition and didn't notice that the wiki page wasn't actually called lincRNA.

The Ensembl definition can be found here:

http://www.ensembl.org/info/docs/genebuild/ncrna.html

We include RNAs that overlap other genes by <35%

[biorepine]

Wiki is right. The original definition came from here http://www.ncbi.nlm.nih.gov/pubmed/19182780. May be you ENSEMBL guys need to change the name from lincRNA to lncRNA. :)