perl api code line meaning
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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
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5e3 is a perl shortcut for 5000.

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

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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.

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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.

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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

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i mean ENSG is genome

what is the meaning of ENSR ?

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ENSG is a gene.

ENSR is a regulatory feature.

Full list of all prefixes here.

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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.

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thank you

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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

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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.

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6.1 years ago

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.