E2F transcription factor meaning in C3

[keremwai]

Within the C3 module, what is the difference between different names of E2F

The names within the C3 module include E2F1_Q6, :E2F_03, E2F1DP1_01, E2F1DP2_01, E2F_Q6,

E2F4DP2_01,  E2F4DP1_01, SGCGSSAAA_E2F1DP2_01,  E2F_Q4, E2F_Q4_01,  E2F_02,  E2F1_Q6_01,  E2F1DP1RB_01,  E2F_Q3_01,  E2F1_Q4_01, E2F_Q6_01,  E2F_01  ,   E2F_Q3,   and more... E2F1_Q3

And I do not understand which of them corresponds to what TF. 

According to the literature there are supposed to be E2F1, E2F2, E2F3 as activators and E2F4-E2F8 as repressors. How do the symbols in C3 respond to the different E2F transcription factors?

I tried to trace it using the original paper, but apparently they send to TRANSFEC paper and the links there are dead. 

Would appreciate your help,

Thank you in advance,

Kerem

[Anthony Castanza]

Hi Kerem,

 

Unfortunately TransFac when to a locked down proprietary model some time ago and the legacy data has become more and more difficult to access, so we've had to move this collection to a "legacy" level and create a new TFT collection from the GTRD dataset. However, this lacks the motif specific data of the old collection due to limitations with the source dataset.
I've reached out to the owners of TransFac to see what's going on with the old public release of the data that should be on the old public site at http://www.gene-regulation.com/pub/databases.html

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Anthony Castanza]

Hello,

I've followed up with the owners of TransFac and they're working on a new hosting solution for the old public database. They weren't able to give an ETA on availability, but confirmed that the downtime is not intentional.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

[keremwai]

Dear Anthony,

Thank you for your answers. It is reassuring that such important information will stay available for the scientific community,.

Could you please point me to who can I ask specifically about these E2F naming?

Thank you for all your help and support,

Kerem

 

ב-יום שישי, 24 בספטמבר 2021 בשעה 01:04:43 UTC+3, Anthony Castanza כתב/ה:

[Anthony Castanza]

Hello,

 

Until the Transfac dataset is back online I found an old archive of the motif data that contains some additional information that appears to have been omitted from the MSigDB release version of these gene sets, for example, E2F_Q6_01 is annotated in this data as corresponding to “

Genes with 3'UTR containing motif NKCGCGCSAAAN which matches annotation for E2F TFDP1: transcription factor Dp-1

Similarly there is additional information for many of the other sets. I’ll add recovering this information to our to-do list for a future MSigDB release, but in the meantime you can access the archive here: Index of /~sayan/genesets/Jan2006/cards/C3.TFAC (duke.edu)

The information you want is in the description field(s) on each of the relevant HTML pages.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

https://gsea-msigdb.org

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/a93f132b-2bb1-4def-b7fd-c343e77e4474n%40googlegroups.com.

 

[Anthony Castanza]

Oh, there’s actually an index page for that archive that should make looking for your sets of interest a little bit easier: C3.TFAC gene sets listing - MSigDB [Broad Insititute] (duke.edu)

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

https://gsea-msigdb.org

 

[keremwai]

Wow Anthony, this is very very helpful!

I've been facing this puzzle for some time and you just gave me the missing peace.

Even If within this index it is not clear what are the exact E2F TF, at least now I can keep exploring using the sequence specific binding site.

Thank you very much!

ב-יום שני, 27 בספטמבר 2021 בשעה 01:17:35 UTC+3, Anthony Castanza כתב/ה: