Availability of mouse cCREs with human orthologues to download

[roxyisat-rex]

Greetings Weng lab members. Firstly thank you for the good work and the great source of data. I have a question about the "Expanded encyclopaedias of DNA elements in the human and mouse genomes"paper.
In the paper there is mentioning of fractions of human and mouse cCREs with homology in the other species.
Within both mouse and human genome, there were some cCREs that map to cCREs in the other genome, which then reciprocally map back to the original genome.
According to the paper, in mouse, for a majority (65%, 158k) of mouse cCREs with human orthologues, the orthologue was also a cCRE, according to Extended Data Fig. 2c. I was wondering if there is a list of these 158k cCREs (mouse homology & cCRE in light blue), in their categories (d/pELS, PLS and CTCF) somewhere available to download? I know there are general tracks of mouse and human cCRE on ENCODE available to view, and also all cCRE in categories to download, but I could not find a list of these conserved ones. I was wondering if these can be provided?

Thank you very much! Looking forward to hearing back.

[roxyisat-rex]

Hi Jill

Thank you for your reply! This card seems to be private? Link says card not found. Could you give me access please? Thank you!

Best wishes, Roxy

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From: Jill Moore @.> Sent: 06 December 2022 13:44 To: weng-lab/SCREEN @.> Cc: Zhang, Roxy @.>; Author @.> Subject: Re: [weng-lab/SCREEN] Availability of mouse cCREs with human orthologues to download (Issue #143)

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[roxyisat-rex]

@Jill-Moore

[Jill-Moore]

Hello @roxyisat-rex.

Thank you for your interest in the Registry of cCREs. Sorry about the "card" above, something must have gone awry with our GitHub/Trello integration.

Linked below are 3 files:

Human cCREs: http://users.wenglab.org/moorej3/ENCODE-cCREs/V2.GRCh38.bed Mouse cCREs: http://users.wenglab.org/moorej3/ENCODE-cCREs/V2.mm10.bed Human-Mouse homology list: http://users.wenglab.org/moorej3/ENCODE-cCREs/V2.Homologous-List.txt

You can use the IDs in the homology list (col 1 human, col 2 mouse) to select for cCREs (col 5 id) & their classifications from the bed files.

Please let me know if you have additional questions.

Many thanks, Jill

[roxyisat-rex]

Hi Jill @Jill-Moore

Thanks for the prompt response! The mouse-human homology list is 404 not found though? Could you send it again please! Sorry for the trouble.

Many thanks, Roxy

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From: Jill Moore @.> Sent: 06 December 2022 14:52 To: weng-lab/SCREEN @.> Cc: Zhang, Roxy @.>; Mention @.> Subject: Re: [weng-lab/SCREEN] Availability of mouse cCREs with human orthologues to download (Issue #143)

This email from @.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Hello @roxyisat-rexhttps://github.com/roxyisat-rex.

Thank you for your interest in the Registry of cCREs. Sorry about the "card" above, something must have gone awry with our GitHub/Trello integration.

Linked below are 3 files:

Human cCREs: http://users.wenglab.org/moorej3/ENCODE-cCREs/V2.GRCh38.bed Mouse cCREs: http://users.wenglab.org/moorej3/ENCODE-cCREs/V2.mm10.bed Human-Mouse homology list: http://users.wenglab.org/moorej3/ENCODE-cCREs/ENCODE-cCREs/V2.Homologous-List.txt

You can use the IDs in the homology list (col 1 human, col 2 mouse) to select for cCREs (col 5 id) & their classifications from the bed files.

Please let me know if you have additional questions.

Many thanks, Jill

— Reply to this email directly, view it on GitHubhttps://github.com/weng-lab/SCREEN/issues/143#issuecomment-1339503093, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AM3QSSNH3YSWSMMLKZHNXULWL5HMHANCNFSM6AAAAAASPS75EE. You are receiving this because you were mentioned.Message ID: @.***>

[Jill-Moore]

Link is fixed above

[roxyisat-rex]

http://users.wenglab.org/moorej3/ENCODE-cCREs/V2.Homologous-List.txt

Thank you very much!