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

[Genomeo Dev]

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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