conflict of enhancer definition between UCSC and screen database

[Tsviya Olender]

Hi

Thanks for all the good work you are investing in your site.

We are trying to use the UCSC genome browser to understand a deletion that we inserted that falls in an enhancer site.

We find that the enhancer in UCSC has a different ID than the one in the SCREEN site. We also find that the genomic coordinates are a bit different. On UCSC, we use hg38, and the screen site is also on hg38.

 

Can you please help us understand the ambiguous information?

 

Many thanks

Tsviya

 

 

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

Can you provide a bit more information about the enhancer that you shared in your screenshot? Where did you find the EH38E2878545 enhancer, and how did you map it to the hg38 assembly?

The SCREEN website has a link to the UCSC Genome Browser, but the session does not include the enhancer that you shared:

https://screen.encodeproject.org/search/?assembly=GRCh38&q=EH38E2878545&uuid=undefined

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr1:244856421-244871679&hubClear=https://screen-beta-api.wenglab.org/ucsc_trackhub/undefined/hub_126.txt&highlight=GRCh38.chr1%3A244863921-244864179

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Jairo Navarro
UCSC Genome Browser

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[Tsviya Olender]

Hi

Thanks for your response.

Yes, the enhancer EH38E2878545 is indeed missing from your site. Please see below.

I extracted the coordinates of the enhancers in the HNRNPU gene region, and uploaded the data into UCSC as a custom track.

I think there are conflicts between the information on your site and on the SCREEN site. Perhaps different versions?

 

Best wishes

Tsviya

 

 

 

 

 

From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Wednesday, July 16, 2025 12:27 AM
To: Tsviya Olender <tsviya....@weizmann.ac.il>
Cc: gen...@soe.ucsc.edu; Shai Fuchs <shai....@weizmann.ac.il>
Subject: Re: [genome] conflict of enhancer definition between UCSC and screen database

 

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[Gerardo Perez]

Hello, Tsviya.

We reached out to the Weng lab regarding the data on their website (https://screen.wenglab.org/) being different from the cCRE track, and they confirmed that their data have been updated since our last update to the cCREs track, which explains the missing EH38E2878545 enhancer annotation from the ENCODE cCREs track.

We are planning to update the cCRE track soon, and in the meantime, you can use the following ENCODE cCRE hub to display the EH38E2878545 enhancer annotation on the Genome Browser: https://users.wenglab.org/moorej3/Registry-cCREs-WG/Track-Hub/hub.txt. Please note that this hub is not maintained by us. Any questions about the hub should be directed to the hub author: jill.eliza...@gmail.com

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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