perl api code line meaning

Question

[naama.levi82]

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?

[Giovanni M Dall'Olio]

5e3 is a perl shortcut for 5000.

[Emily]

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

[SES]

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.

Answer 1

[Emily]

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.

[naama.levi82]

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

[naama.levi82]

I mean ENSG is genome

What is the meaning of ENSR?

[Emily]

ENSG is a gene.

ENSR is a regulatory feature.

Full list of all prefixes here.

[Emily]

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.

[naama.levi82]

Thank you

[naama.levi82]

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

[Emily]

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.

Answer 2

[GouthamAtla]

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.