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 mean?
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.
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
Thanks
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.
Thank you
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
Thanks again
Here is 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.
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.
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5e3 is a perl shortcut for 5000.
ie, it means 5 x 10^3, ie 5000
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.