[ensembl-dev] Variation::OverlapConsequence::rank()

[Will McLaren]

Seems nc_transcript_variant is out of order in that table, thanks for
spotting that.

ConsequenceType.pm is not used by the current API code and will be
deprecated. The Ensembl terms are no longer the preferred terms to use; the
SO equivalents are what we recommend for use now.

You can get the consequence types and their various attributes from the
hash:

%Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES

e.g. to get a hash with the ranks in:

my %ranks = map {$_->SO_term => $_->rank} values
%Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES;

print "$_\t$ranks{$_}\n" for sort {$ranks{$a} <=> $ranks{$b}} keys %ranks;

Regards

Will


On 30 May 2014 10:21, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi Will,
>
> I wonder if that is the latest table as seems not consistent with these
> ranks obtained from OverlapConsequence::rank()
>
> 21 INTRONIC
> 22 NMD_TRANSCRIPT
> 23 WITHIN_NON_CODING_GENE
> 24 UPSTREAM
> 25 DOWNSTREAM
> 36 REGULATORY_REGION
> 38 INTERGENIC
>
> In particular ranks 36 and 38 go beyond the number of entries in that
> table. Also note that in ConsequenceType.pm, there are fewer ensembl
> display terms compared to those shown under 'old Ensembl terms' in the
> table, in case those are meant to be the same:
>
> our %CONSEQUENCE_DESCRIPTIONS = (
>   'ESSENTIAL_SPLICE_SITE'  => 'In the first 2 or the last 2 basepairs of
> an intron',
>   'STOP_GAINED'            => 'In coding sequence, resulting in the gain
> of a stop codon',
>   'STOP_LOST'              => 'In coding sequence, resulting in the loss
> of a stop codon',
>   'COMPLEX_INDEL'          => 'Insertion or deletion that spans an
> exon/intron or coding sequence/UTR border',
>   'FRAMESHIFT_CODING'      => 'In coding sequence, resulting in a
> frameshift',
>   'NON_SYNONYMOUS_CODING'  => 'In coding sequence and results in an amino
> acid change in the encoded peptide sequence',
>   'SPLICE_SITE'            => '1-3 bps into an exon or 3-8 bps into an
> intron',
>   'PARTIAL_CODON'          => 'Located within the final, incomplete codon
> of a transcript whose end coordinate is unknown',
>   'SYNONYMOUS_CODING'      => 'In coding sequence, not resulting in an
> amino acid change (silent mutation)',
>   'REGULATORY_REGION'      => 'In regulatory region annotated by Ensembl',
>   'WITHIN_MATURE_miRNA'    => 'Located within a microRNA',
>   '5PRIME_UTR'             => 'In 5 prime untranslated region',
>   '3PRIME_UTR'             => 'In 3 prime untranslated region',
>   'INTRONIC'               => 'In intron',
>   'NMD_TRANSCRIPT'         => 'Located within a transcript predicted to
> undergo nonsense-mediated decay',
>   'WITHIN_NON_CODING_GENE' => 'Located within a gene that does not code
> for a protein',
>   'UPSTREAM'               => 'Within 5 kb upstream of the 5 prime end of
> a transcript',
>   'DOWNSTREAM'             => 'Within 5 kb downstream of the 3 prime end
> of a transcript',
>   'HGMD_MUTATION'          => 'Mutation from the HGMD database -
> consequence unknown',
>   'INTERGENIC'             => 'More than 5 kb either upstream or
> downstream of a transcript',
> );
>
> Regards,
>
> G.
>
>
> On 30 May 2014 09:50, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
>> Hello,
>>
>> The ranks are given in this table:
>>
>>
>> http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences
>>
>> Regards
>>
>> Will
>>
>>
>> On 29 May 2014 17:26, Genomeo Dev <genomeodev at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> The method Bio::EnsEMBL::Variation::OverlapConsequence::rank() seems to
>>> return 'the relative rank of this OverlapConsequence when compared to other
>>> OverlapConsequence objects. This is used, for example, to determine the
>>> most severe consequence of a VariationFeature".
>>>
>>> As shown in this example each consequence term appears to have a unique
>>> rank independently of the collective consequence terms for the input
>>> variant. Is there a dictionary somewhere of ranks and corresponding terms?
>>>
>>> Location Allele Existing_variation SYMBOL SYMBOL_SOURCE Gene ENSP
>>> Feature Feature_type BIOTYPE STRAND CANONICAL EXON INTRON DISTANCE
>>> TSSDistance FeatureDistance Consequence Effect Rank
>>> 2:208228309 T rs17808606 AC007879.5 Clone_based_vega_gene
>>> ENSG00000223725 - ENST00000412387 Transcript antisense -1 - - 3/4 - - 0
>>> intron_variant,nc_transcript_variant INTRONIC,WITHIN_NON_CODING_GENE
>>> 21,23
>>> 2:208231478 T rs17808718 AC007879.5 Clone_based_vega_gene
>>> ENSG00000223725 - ENST00000412387 Transcript antisense -1 - - 3/4 - - 0
>>> intron_variant,nc_transcript_variant INTRONIC,WITHIN_NON_CODING_GENE
>>> 21,23
>>> 2:208440836 C rs17811997 CREB1 HGNC ENSG00000118260 ENSP00000412016
>>> ENST00000418081 Transcript nonsense_mediated_decay 1 - - 5/8 - - 0
>>> intron_variant,NMD_transcript_variant INTRONIC,NMD_TRANSCRIPT 21,22
>>>
>>> Thanks,
>>>
>>> --
>>> G.
>>>
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>>
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>
>
> --
> G.
>
> _______________________________________________
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