[ensembl-dev] Variation::OverlapConsequence::rank()
Genomeo Dev
genomeodev at gmail.com
Mon Jun 2 13:03:20 BST 2014
Thanks. Actually the terms in ConsequenceType.pm are quite a useful
grouping for a broad classification. I would love to see them at least in
the API in future releases as it would make a good common ground for those
reporting broad variant consequences.
G.
On 30 May 2014 11:52, Laurent Gil <lgil at ebi.ac.uk> wrote:
> Hi Genomeo,
>
> Actually it's because the terms are grouped by the Old Ensembl term, using
> the highest rank of the terms which belong to this "group",
> e.g:
> The Old Ensembl term " Within non coding gene" should be ranked 23 but the
> term " non_coding_exon_variant" is ranked 20, so we displayed it in the
> table at the rank 20.
>
> Thanks for spotting that. We built the table a long time ago and it
> definitively need to be updated.
> We will change the table in the next release to match the ranking of each
> individual consequence term.
>
> Best regards,
>
> Laurent
>
> On 30/05/2014 11:41, Will McLaren wrote:
>
> 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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>
>
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--
G.
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