[ensembl-dev] Missmatch from database and website

[Mahmood Naderan]

Hi Mag,
Some of my questions were answered, though some new questions arose. For
example, what is the difference between fetch_all_by_external_name and
fetch_all_by_display_name. The descriptions in core document seems to be
similar and I can not find where should I use the first and where should I
use the second.


Regards,
Mahmood



On Mon, Jul 17, 2017 at 7:02 PM, mag <mr6 at ebi.ac.uk> wrote:

> Hi Mahmood,
>
> The fetch_all_by_external_name returns a list of genes for which atxn3 is
> an associated link.
> For GRCh37, there are two genes which qualify, as can be seen on the
> search page:
> http://grch37.ensembl.org/Homo_sapiens/Search/Results?q=
> atxn3;site=ensembl_all;page=1;facet_feature_type=Gene;facet_species=Human
> If you check the second element of the list, you will get ENSG00000066427
>
> For ENSG00000259634, atxn3 is not the main display name, but it has a link
> to the corresponding NCBIgene entry for atxn3.
> http://grch37.ensembl.org/Homo_sapiens/Gene/Matches?db=
> core;g=ENSG00000259634;r=14:92523341-92575863;t=ENST00000558190
>
> If you are only interested in genes for which atxn3 is the chosen symbol,
> you can use the fetch_all_by_display_label method instead.
>
> However, please be aware that the fetch_all_by_display_label will still
> return a list of genes, which could have more than one element.
> For example, two genes can share the same name if one is on the reference
> while the other one is on a haplotype.
> There are also cases where a name is misassigned to a gene, resulting in a
> duplication. This can happen when two genes are overlapping.
>
> Because of this, I would recommend looping through the resulting list
> rather than assume the first result is the one you want.
> You can then check for various gene attributes to ensure this is the one
> you expect.
>
>
> Hope that helps,
> Magali
>
>
>
> On 15/07/2017 12:55, Mahmood Naderan wrote:
>
> I have an update that may shed a light but I cannot figure out.
> With the command in my previous email, I see that the stableID is
> ENSG00000259634. As I enter this ID in the web site, I see
>
> Gene: RP11-529H20.5 ENSG00000259634  . Location  Chromosome 14:
> 92,524,896-92,525,877 reverse strand.
>
> As you can see the start and end numbers matches with my previous email
> and its name is not ATXN3 which I requested in the command. So, the
> question is that why fetch_all_by_external_name("atxn3") returns that.
>
> In my previous questions, Emily pointed that function may returns LRGs.
> For me it is hard to understand since I am not an expert in that field. I
> want to the get the main gene and not anything else.
>
> Regards,
> Mahmood
>
>
>
> On Sat, Jul 15, 2017 at 2:15 PM, Mahmood Naderan <mahmood.nt at gmail.com>
> wrote:
>
>> Hi,
>> With this code
>>
>>   my @genes = @{ $gene_adaptor->fetch_all_by_external_name("atxn3) };
>>   my $gene  = @genes[0];
>>   my $start = $gene->start();
>>   my $end   = $gene->end();
>>
>> I see that
>>   start=92524896
>>   end=92525877
>>
>> However, from the website, I see
>>   Chromosome 14: 92,524,896-92,572,965
>>
>> As you can see, the end numbers are different.
>> http://grch37.ensembl.org/Homo_sapiens/Gene/Sequence?db=core
>> ;g=ENSG00000066427;r=14:92524896-92572965
>>
>>
>> Is there any reason for that?
>>
>> Regards,
>> Mahmood
>>
>>
>>
>
>
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