Question: perl api code line meaning
0
gravatar for naama.levi82
4.5 years ago by
European Union
naama.levi820 wrote:

 my $slice = $slice_adaptor->fetch_by_gene_stable_id( 'ENSG00000099889', 5e3 );

where does it look for ?

what does it bring ?

when the code is running i have this results : 

3. Investigate what regulatory elements are returned:

        Feature Type: TF binding site

ENSR00001041428:        Cell: MultiCell

        Feature Type: Enhancer

ENSR00000672895:        Cell: MultiCell

        Feature Type: CTCF

ENSR00000169383:        Cell: MultiCell

        Feature Type: Enhancer

ENSR00000291472:        Cell: MultiCell

 

what does it's mean? 

forum ensembl gene • 1.1k views
ADD COMMENTlink modified 4.5 years ago by SES8.2k • written 4.5 years ago by naama.levi820
1

5e3 is a perl shortcut for 5000.

ADD REPLYlink written 4.5 years ago by Giovanni M Dall'Olio26k
1

ie, it means 5 x 10^3, ie 5000

ADD REPLYlink written 4.5 years ago by Emily_Ensembl18k

For reference, it's not a Perl thing, it is scientific notation and the syntax is the same in most programming languages and calculators. I recognize that in the context of an API the meaning could be lost though.

ADD REPLYlink written 4.5 years ago by SES8.2k
2
gravatar for Emily_Ensembl
4.5 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

The slice adaptor is getting a slice, or region of the genome. In this case, it's finding a gene (ENSG00000099889) and adding on some 5kb flanks to either side (5e3).

Presumably you've been gifted with a script and you're not sure how it works.

ADD COMMENTlink written 4.5 years ago by Emily_Ensembl18k

I'm trying to understand how does ensemble Ensembl work 

can you please explain to me what does these result of the code mean? 

        Feature Type: TF binding site

ENSR00001041428:        Cell: MultiCell

        Feature Type: Enhancer

ENSR00000672895:        Cell: MultiCell

        Feature Type: CTCF

ENSR00000169383:        Cell: MultiCell

thank's 

 

ADD REPLYlink modified 4.5 years ago by Emily_Ensembl18k • written 4.5 years ago by naama.levi820

i mean ENSG is genome 

what is the meaning of ENSR ? 

 

ADD REPLYlink written 4.5 years ago by naama.levi820

ENSG is a gene.

ENSR is a regulatory feature.

Full list of all prefixes here.

ADD REPLYlink written 4.5 years ago by Emily_Ensembl18k

Your code has returned some regulatory features within the region that you defined with the slice. For example ENSR00000672895 is a CTCF binding site. These features are determined using the Ensembl regulatory build. This video is also helpful in explaining this.

ADD REPLYlink written 4.5 years ago by Emily_Ensembl18k

thank you 

ADD REPLYlink written 4.5 years ago by naama.levi820

Hi again 

i have one more question: 

in ensmbl site under the category: 

The Ensembl Regulatory Build on human. 

Segmentation and annotation of segmentation states.

they wrote: "We start by running a segmentation across all possible cell-types "

what is the intention of all possible cell types? which cell types 

thank's again 

ADD REPLYlink written 4.5 years ago by naama.levi820

Here's a list of all the current cell types. Segmentation is run for each cell type individually, not over a combined data set. It is done on each cell type where there is sufficient data to do so - the limit is having a marker of open chromatin (eg DNase sensitivity or FAIRE), CTCF ChIP-seq and ChIP-seq for H3K4me3, H3K27me3, H3K36me3 histone modifications.

ADD REPLYlink written 4.5 years ago by Emily_Ensembl18k
0
gravatar for geek_y
4.5 years ago by
geek_y9.8k
Barcelona
geek_y9.8k wrote:

Read this tutorial http://asia.ensembl.org/info/docs/api/core/core_tutorial.html?redirect=no

ENSG00000099889 is a gene id and 5e3 is length of flanking sequence

I am not sure but I think you are getting all the annotations that are located within 5K region of that gene.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by geek_y9.8k
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