Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

A single HT-SELEX motif has two different names in the factorbook database #2

Open
Yaqiao-Li opened this issue Mar 16, 2023 · 7 comments
Open

A single HT-SELEX motif has two different names in the factorbook database #2

Yaqiao-Li opened this issue Mar 16, 2023 · 7 comments

Comments

@Yaqiao-Li
Copy link

Yaqiao-Li commented Mar 16, 2023 •
edited
Loading

Hi Team,

Recently I meet a problem when using the dataset of HT-SELEX motifs.
A single motif in HT-SELEX datset in the factorbook database has two different names from the two download resource:

  1. Download from HT-SELEX Catalog https://downloads.wenglab.org/factorbook-download/all-selex-motifs.meme.gz
  2. Download by click the "export motif(MEME)" button on the Transcription factor webpage, for example https://www.factorbook.org/tf/human/CTCF/deeplearnedselexmotif

For example, in the file all-selex-motifs.meme.gz downloaded from HT-SELEX Catalog, there is a motif named "ERR173155", but there is no information about the Transcription Factor for this motif(usually in some databases like JASPAR, the TF info will be contained in the motif name).


'''
MOTIF ERR173155
letter-probability matrix: alength= 4 w= 12 nsites= 49 E= 0
0.1129  0.0928  0.6914  0.1029
0.1179  0.6925  0.0936  0.0960
0.0117  0.9701  0.0081  0.0101
0.4128  0.5225  0.0296  0.0351
0.0186  0.7485  0.0059  0.2271
0.0118  0.9670  0.0113  0.0098
0.0391  0.0254  0.0376  0.8979
0.6195  0.0573  0.1971  0.1261
0.0740  0.1985  0.6007  0.1268
0.0851  0.3797  0.0467  0.4885
0.0364  0.0318  0.8863  0.0456
0.1007  0.0616  0.6782  0.1595
'''

Actually, it is the first motif of CTCF, if we downloaded by click the "export motif(MEME)" button on this webpage https://www.factorbook.org/tf/human/CTCF/deeplearnedselexmotif, this motif has got a new name "Jolma-2013".

'''
MEME version 4.5
ALPHABET= ACGT

MOTIF Jolma-2013_
letter-probability matrix: alength= 4 w= 12 nsites= 0 E= 0
0.1129 0.0928 0.6914 0.1029
0.1179 0.6925 0.0936 0.0960
0.0117 0.9701 0.0081 0.0101
0.4128 0.5225 0.0296 0.0351
0.0186 0.7485 0.0059 0.2271
0.0118 0.9670 0.0113 0.0098
0.0391 0.0254 0.0376 0.8979
0.6195 0.0573 0.1971 0.1261
0.0740 0.1985 0.6007 0.1268
0.0851 0.3797 0.0467 0.4885
0.0364 0.0318 0.8863 0.0456
0.1007 0.0616 0.6782 0.1595
'''

Is there a special reason for setting different names for the same motif?

Another question related is, do you have a table for looking up the Transcription factor name of the motif?
I downloaded the <all-selex-motifs.meme.gz> and found some motifs as candidates for the next step of our research, but get stuck here because it is hard to find out which transcription factor the motifs belong to.

For example, by directly searching with the name "ERR173155" in the database, we can't get the right result. By searching with the matrix, it will match some similar motifs but not exactly the same one. May I get some suggestions from you on how to find out the TF of each motif in the HT-SELEX catalog?

Thank you!
Looking forward to your reply!
@grandrews
Copy link

grandrews commented Mar 17, 2023 via email

@Yaqiao-Li
Copy link
Author

Hi Greg,

Thank you so much! This text file of HT-SELEX accession 'ERR' number and the TF is really helpful. But it seems incomplete, ending up with "MYBL2 ERR" as the last line. Could you please look into that?

Thank you!

Yaqiao

@grandrews
Copy link

grandrews commented Mar 20, 2023 via email

@Yaqiao-Li
Copy link
Author

Yaqiao-Li commented Mar 20, 2023 via email

@YozonChen
Copy link

Hi team

I recently encountered a similar problem as Yaoqiao when using HT-SELEX data. Could you please also send the text file to my email? yozonchen AT gmail.com.Thank you very much!

Yozon

@grandrews
Copy link

grandrews commented Jun 5, 2024 via email

@YozonChen
Copy link

Hi Greg！

Yes, this is exactly what I was looking for. However,it still cannot be displayed correctly on the website.Can you directly send the file to my email? yozonchen AT gmail.com

Thank you so much!

Yozon

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@grandrews @Yaqiao-Li @YozonChen