perl api code line meaning
2
0
Entering edit mode
6.1 years ago

 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? 

gene Forum ensembl • 1.3k views
ADD COMMENT
1
Entering edit mode

5e3 is a perl shortcut for 5000.

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
2
Entering edit mode
6.1 years ago

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

i mean ENSG is genome 

what is the meaning of ENSR ? 

 

ADD REPLY
0
Entering edit mode

ENSG is a gene.

ENSR is a regulatory feature.

Full list of all prefixes here.

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

thank you 

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode
6.1 years ago

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 COMMENT

Login before adding your answer.

Traffic: 1951 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6