[ensembl-dev] Gata1

Daniel Sobral sobral at ebi.ac.uk
Mon Aug 8 18:50:02 BST 2011


Hi Thomas,

We have one dataset for Gata1 from ENCODE in Ensembl. We have initially 
included this set, as it is for K562, but we later excluded it from our 
regulatory build for K562, because it is using an alternative K562 
cell-line (K562b) different from the other K562. You can see more 
details on the ENCODE cell-lines here: 
http://genome.ucsc.edu/ENCODE/cellTypes.html

Since we do not include it in our regulatory build, you cannot access 
the Gata1 data the standard way (from the Regulatory Features).
But the data is still valid, and we kept it in the database, so you can 
access it directy via its set name.
(you can have a list of all available set names from the featureset adaptor)

Here's some example code to access Gata1 sites. Be aware nonetheless 
that datasets not included in the regulatory build are considered 
deprecated and may be removed / changed in the future.

my $fset_adaptor = $registry->get_adaptor('Homo sapiens', 'funcgen', 
'featureset');

my $gata1_fset = 
$fset_adaptor->fetch_by_name("K562b_Gata1_ENCODE_Yale_SWEMBL_R015");

@gata1_feats = @{$gata1_fset->get_Features_by_Slice($slice)};

foreach my $gata_feat (@gata1_feats){
     my @motifs = @{$gata_feat->get_associated_MotifFeatures()};
     foreach my $motif (@motifs){
         print 
$motif->seq_region_name."\t".$motif->seq_region_start."\t".$motif->seq_region_end."\t".
             
$motif->seq_region_strand."\t".$motif->score."\t".$motif->binding_matrix->name."\n";
     }
}


Hope it helps,
Daniel

On 08/08/2011 09:35, David Thomas wrote:
> Hi
>
> I'm trying to extract specific TFBS information using the funcgen API. I can find most of the information I need but nothing on Gata1.
>
> I drill down as follows:
>
> @reg_feats = @{$regfeat_adaptor->fetch_all_by_Slice($slice)};
> foreach my $rf (@reg_feats){
> 	…..	
> 	foreach my $feature (@{$rf->regulatory_attributes()}){
> 		….
> 		my @motif_features = @{$rf->regulatory_attributes('motif')};
> 		foreach my $motif_feature (@motif_features) {
> 			……
> 			my $afs = $motif_feature->associated_annotated_features();	
> 	 		foreach my $feat (@$afs){
> 				.....
>
> Looking at the displaylabels in each of the levels I can find no information on Gata1.
>
> Apologies if this is a naive question but any help gratefully received.
>
> David
>
>
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