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JASPAR Q&A Forum
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Hello!
Welcome to the
JASPAR
Q&A forum.
The latest version of JASPAR is available at
http://jaspar.genereg.net
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Team JASPAR
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Sandra Silva
Jul 19
Find THR binding sites on some genes of interest
Hi all, In my research, I found some candidate genes and now I would like to know if these genes are
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Find THR binding sites on some genes of interest
Hi all, In my research, I found some candidate genes and now I would like to know if these genes are
Jul 19
Baiguang Yu
Jul 9
How to find miRNAs' TF in JASPAR?
Hello! How to find miRNAs' TF in JASPAR? If you could give me the pictures,that would be very
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How to find miRNAs' TF in JASPAR?
Hello! How to find miRNAs' TF in JASPAR? If you could give me the pictures,that would be very
Jul 9
Abdullah Khasawneh
Jul 6
Finding all (possible) targets of a TF
Hello. Thanks for all your efforts to make JASPAR. I have a list of transcription factors, enriched
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Finding all (possible) targets of a TF
Hello. Thanks for all your efforts to make JASPAR. I have a list of transcription factors, enriched
Jul 6
Victor Levitsky
Jun 10
NRF1
Dear Jaspar team! I found the error in your annotation - https://jaspar.uio.no/matrix/MA0506.2/ is
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NRF1
Dear Jaspar team! I found the error in your annotation - https://jaspar.uio.no/matrix/MA0506.2/ is
Jun 10
Tanay Ghosh
May 18
JASPAR version
How to find older JASPAR version. I earlier used JASPAR v. 2016 and would like to reproduce my data
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JASPAR version
How to find older JASPAR version. I earlier used JASPAR v. 2016 and would like to reproduce my data
May 18
David N Levy
, …
Oriol Fornés
3
May 11
Human Stat5
When in doubt, you can always use the profile inference tool: https://jaspar.genereg.net/inference I
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Human Stat5
When in doubt, you can always use the profile inference tool: https://jaspar.genereg.net/inference I
May 11
Danielle Hiam
May 9
Selecting distance upstream and downstream of TSS for enrichment analysis
Hello, I have list of 97 DE genes from a RNAseq experiment that I would like to investigate if any
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Selecting distance upstream and downstream of TSS for enrichment analysis
Hello, I have list of 97 DE genes from a RNAseq experiment that I would like to investigate if any
May 9
Aleksandra Kurowska
,
Anthony Mathelier
2
Mar 29
TFBS download
Dear Aleksandra, Thanks for your interest in JASPAR. The 274 profiles you are referring to were
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TFBS download
Dear Aleksandra, Thanks for your interest in JASPAR. The 274 profiles you are referring to were
Mar 29
Laura Ponting
,
Anthony Mathelier
2
Mar 1
Splice collection removal
Dear Laura, Thanks for your enquiry. In the latest JASPAR release, we discarded unused collections
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Splice collection removal
Dear Laura, Thanks for your enquiry. In the latest JASPAR release, we discarded unused collections
Mar 1
hanwen yu
,
Anthony Mathelier
2
Feb 21
Generate my own JASPAR SQLite file
Dear Hanwen, We currently do not provide this functionality. I guess you should add your motifs
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Generate my own JASPAR SQLite file
Dear Hanwen, We currently do not provide this functionality. I guess you should add your motifs
Feb 21
Brendan Rooney
,
Anthony Mathelier
2
Feb 20
Confirming how to identify putative TF binding sites
Hi Brendan, Yes, you are correct. I would suggest that you use our set of predefined TFBSs provided
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Confirming how to identify putative TF binding sites
Hi Brendan, Yes, you are correct. I would suggest that you use our set of predefined TFBSs provided
Feb 20
Nguyen Xuan-Thang
,
Anthony Mathelier
2
Feb 16
List of TFs gene name and protein name
Hi Thang, Thanks for your interest in JASPAR. The TF gene names are provided in the metadata, which
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List of TFs gene name and protein name
Hi Thang, Thanks for your interest in JASPAR. The TF gene names are provided in the metadata, which
Feb 16
Muhammad Danial
,
Anthony Mathelier
2
11/18/22
How to Download PWM of Ctcf
Click on one of the IDs (they point to the links I gave you in another thread) and then you can
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How to Download PWM of Ctcf
Click on one of the IDs (they point to the links I gave you in another thread) and then you can
11/18/22
Rosanna Di Tinco
, …
Anthony Mathelier
4
11/17/22
How to find TFs starting from promoter region
As I wrote above, you can download the BED files to look for overlap in your region of interest. We
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How to find TFs starting from promoter region
As I wrote above, you can download the BED files to look for overlap in your region of interest. We
11/17/22
Cassandre Coles
, …
Anthony Mathelier
8
11/17/22
Re: Is there any way to display the highest possible score and relative score for a TFBS
Hi Danial, We have 3 PFMs from CTCF: https://jaspar.genereg.net/matrix/MA0139.1/, https://jaspar.
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Re: Is there any way to display the highest possible score and relative score for a TFBS
Hi Danial, We have 3 PFMs from CTCF: https://jaspar.genereg.net/matrix/MA0139.1/, https://jaspar.
11/17/22
dcamer...@gmail.com
,
Anthony Mathelier
3
11/7/22
Jaspar Enrichment missing allEnrichment.tsv output
Hi Anthony, I apologize for the delayed response. I am attempting to restart the process from the
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Jaspar Enrichment missing allEnrichment.tsv output
Hi Anthony, I apologize for the delayed response. I am attempting to restart the process from the
11/7/22
Jessica McAnulty
,
Oriol Fornés
5
9/22/22
Profile Interference Tool
Hi Jessica, I have to update the documentation on GitHub, but I have implemented what you requested.
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Profile Interference Tool
Hi Jessica, I have to update the documentation on GitHub, but I have implemented what you requested.
9/22/22
Malcolm Cook
,
Anthony Mathelier
2
9/5/22
Incorrect link: Cluster-wise Motif Files
Thanks so much for pointing that out. We will fix that asap. Best AM On Wednesday, August 31, 2022 at
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Incorrect link: Cluster-wise Motif Files
Thanks so much for pointing that out. We will fix that asap. Best AM On Wednesday, August 31, 2022 at
9/5/22
Malcolm Cook
,
Anthony Mathelier
3
9/5/22
mal-formed RSAT matrix clusters for JASPAR 2022 Invertebrates !?! (NOT)
Thanks very much for pointing that you. We'll address this as you suggest to make it clearer. On
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mal-formed RSAT matrix clusters for JASPAR 2022 Invertebrates !?! (NOT)
Thanks very much for pointing that you. We'll address this as you suggest to make it clearer. On
9/5/22
Effie Klimi
,
Anthony Mathelier
2
8/30/22
jaspar enrichment analysis - xargs error
Hi Effie, Thanks for your request. It seems the OSX xargs does not allow for long options (see https:
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jaspar enrichment analysis - xargs error
Hi Effie, Thanks for your request. It seems the OSX xargs does not allow for long options (see https:
8/30/22
Malcolm Cook
,
Anthony Mathelier
2
8/26/22
cannot verify jaspar2022.genereg.net's certificate, issued by ‘/C=US/O=Let's Encrypt/CN=R3’:
Thanks very much for the info. Best AM On Friday, August 19, 2022 at 9:29:31 PM UTC+2 malcol...@gmail
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cannot verify jaspar2022.genereg.net's certificate, issued by ‘/C=US/O=Let's Encrypt/CN=R3’:
Thanks very much for the info. Best AM On Friday, August 19, 2022 at 9:29:31 PM UTC+2 malcol...@gmail
8/26/22
Malcolm Cook
,
Anthony Mathelier
2
8/26/22
mysql now sqlite3
Dear Malcolm, Thanks for your interest in JASPAR. We have moved our local instance to sqlite for
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mysql now sqlite3
Dear Malcolm, Thanks for your interest in JASPAR. We have moved our local instance to sqlite for
8/26/22
Malcolm Cook
,
Oriol Fornés
3
8/11/22
sox3 motif changes unrecorded ??
Indeed - thanks for the correction and tip. On Thursday, August 11, 2022 at 4:14:06 PM UTC-5 oriol...
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sox3 motif changes unrecorded ??
Indeed - thanks for the correction and tip. On Thursday, August 11, 2022 at 4:14:06 PM UTC-5 oriol...
8/11/22
Sharon Torigoe
,
Anthony Mathelier
2
6/6/22
Using JASPAR for publications
Hi Sharon, Of course, that's no problem at all as long as the JASPAR paper is appropriately cited
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Using JASPAR for publications
Hi Sharon, Of course, that's no problem at all as long as the JASPAR paper is appropriately cited
6/6/22
Peter Cockerill
,
anthony....@gmail.com
2
5/31/22
motif MA1621.1 binds to Ptf1a and not to Rbpj or Rbpjl. You need to relabel this motif as Ptf1a.
Thank you very much for raising this issue. I agree with you and we will fix this issue asap. On
unread,
motif MA1621.1 binds to Ptf1a and not to Rbpj or Rbpjl. You need to relabel this motif as Ptf1a.
Thank you very much for raising this issue. I agree with you and we will fix this issue asap. On
5/31/22
Selam Solomon
,
anthony....@gmail.com
2
5/5/22
TF protein sequences
Dear Selam, We do not provide that unfortunately. On Friday, April 29, 2022 at 10:50:25 AM UTC+2
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TF protein sequences
Dear Selam, We do not provide that unfortunately. On Friday, April 29, 2022 at 10:50:25 AM UTC+2
5/5/22
Laura Farr
, …
anthony....@gmail.com
4
5/5/22
"Familial profile #" in UCSC browser
Dear Wojciech, You have a good point here. We provide the mapping but in a non-parsable way, which is
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"Familial profile #" in UCSC browser
Dear Wojciech, You have a good point here. We provide the mapping but in a non-parsable way, which is
5/5/22
Nusrat Hossain
,
anthony....@gmail.com
2
4/28/22
webpage loading issue
Sorry for the delayed reply. I assume it has been fixed now. On Tuesday, July 27, 2021 at 6:30:20 PM
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webpage loading issue
Sorry for the delayed reply. I assume it has been fixed now. On Tuesday, July 27, 2021 at 6:30:20 PM
4/28/22
Orsolya Liska
,
anthony....@gmail.com
2
4/28/22
assembly versions of TF binding sites
Unfortunately, these BED files were created too long ago and the assembly version was not recorded
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assembly versions of TF binding sites
Unfortunately, these BED files were created too long ago and the assembly version was not recorded
4/28/22
Tania Cid
,
anthony....@gmail.com
2
4/28/22
Negative score
Hi Tania, The score corresponds to the PWM score, which is the sum of positive and negative scores in
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Negative score
Hi Tania, The score corresponds to the PWM score, which is the sum of positive and negative scores in
4/28/22