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Hello!
Welcome to the
JASPAR
Q&A forum.
The latest version of JASPAR is available at
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ttps://
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Team JASPAR
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Ambuj Kumar
,
Anthony Mathelier
5
May 18
Clarification on JASPAR IDs MA0668.3 vs MA1993.2 for Neurod2
The base ID is associated with a specific motif for a TF. JASPAR provides binding profiles per taxon,
unread,
Clarification on JASPAR IDs MA0668.3 vs MA1993.2 for Neurod2
The base ID is associated with a specific motif for a TF. JASPAR provides binding profiles per taxon,
May 18
Timothy Bailey
,
Anthony Mathelier
2
May 9
Could you create "jaspar2024.genreg.net" links for JASPAR 2024 matrices?
Hi Tim. Thanks for your message, support, and query. That is a very good suggestion indeed. We will
unread,
Could you create "jaspar2024.genreg.net" links for JASPAR 2024 matrices?
Hi Tim. Thanks for your message, support, and query. That is a very good suggestion indeed. We will
May 9
Sager Gosai
,
Anthony Mathelier
2
May 9
Triggered Captcha
The captcha is expected here since it is associated with a form for users to provide us support for
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Triggered Captcha
The captcha is expected here since it is associated with a form for users to provide us support for
May 9
Promit Ganguly
,
Anthony Mathelier
2
May 9
Query regarding the JASPAR enrichment analysis
The Y-axis should be labeled -log10(pvalue). Thanks for raising the issue. On Monday, November 18,
unread,
Query regarding the JASPAR enrichment analysis
The Y-axis should be labeled -log10(pvalue). Thanks for raising the issue. On Monday, November 18,
May 9
Romain Giraud
,
Anthony Mathelier
2
May 9
Different species for different versions of TFBS
Hi Romain. JASPAR is species agnostic within the same taxon. If you are interesting in mouse TFBSs,
unread,
Different species for different versions of TFBS
Hi Romain. JASPAR is species agnostic within the same taxon. If you are interesting in mouse TFBSs,
May 9
yx zhu
,
Anthony Mathelier
2
May 9
backgroud model
Hi. We do not provide any background but the raw PFMs. You can transform the PFMs into PWMs with the
unread,
backgroud model
Hi. We do not provide any background but the raw PFMs. You can transform the PFMs into PWMs with the
May 9
Cen T
,
Ieva Rauluseviciute
2
May 2
PAX3:FKHR fusion motif
Dear Cen, In order to include this motif, we need TF-DNA interaction data, such as ChIP-seq or HT-
unread,
PAX3:FKHR fusion motif
Dear Cen, In order to include this motif, we need TF-DNA interaction data, such as ChIP-seq or HT-
May 2
Radka Symonova
Apr 15
search for collaboration on TFs of juvenile fish brains
Dear JASPAR community, since i am totally new in the research of TFs, I would like to find help or
unread,
search for collaboration on TFs of juvenile fish brains
Dear JASPAR community, since i am totally new in the research of TFs, I would like to find help or
Apr 15
Anthony Mathelier
Jan 16
JASPAR survey
Dear colleagues and JASPAR users, We are conducting a survey to further improve JASPAR by
unread,
JASPAR survey
Dear colleagues and JASPAR users, We are conducting a survey to further improve JASPAR by
Jan 16
Menglin Li
2
11/21/24
TFBS extraction tool vs. web scanning function
I noticed there is another tool developed (https://github.com/wassermanlab/JASPAR-UCSC-tracks), I saw
unread,
TFBS extraction tool vs. web scanning function
I noticed there is another tool developed (https://github.com/wassermanlab/JASPAR-UCSC-tracks), I saw
11/21/24
samirah rokib
, …
Menglin Li
3
11/20/24
Scores
Hi Oriol, Thanks for your information on the relative score! I just wonder how the "score"
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Scores
Hi Oriol, Thanks for your information on the relative score! I just wonder how the "score"
11/20/24
Melanie Fattohi
, …
Menglin Li
3
11/20/24
scan for motifs in TFBS
Hi Anthony, I used the TFBS extraction tool to get the score and I noticed that the score I got is P-
unread,
scan for motifs in TFBS
Hi Anthony, I used the TFBS extraction tool to get the score and I noticed that the score I got is P-
11/20/24
Irene Vides Urrestarazu
2
11/18/24
How do I interpret the score number of the predictions after scanning a TF vs a promoter sequence?
This is the result i got. Thank you in advance!! El lunes, 18 de noviembre de 2024 a las 20:21:43 UTC
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How do I interpret the score number of the predictions after scanning a TF vs a promoter sequence?
This is the result i got. Thank you in advance!! El lunes, 18 de noviembre de 2024 a las 20:21:43 UTC
11/18/24
王晓
, …
Anthony Mathelier
4
11/1/24
The JASPAR database data is incomplete
Thanks for the inquiry. As I previously wrote, we are not convinced that MECP2 is a DNA-binding-
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The JASPAR database data is incomplete
Thanks for the inquiry. As I previously wrote, we are not convinced that MECP2 is a DNA-binding-
11/1/24
S. Hoyer
,
Anthony Mathelier
2
11/1/24
Inquiry Regarding Missing Collections in JASPAR 2024
In the 9th release of JASPAR, we discarded unused collections introduced in early releases of the
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Inquiry Regarding Missing Collections in JASPAR 2024
In the 9th release of JASPAR, we discarded unused collections introduced in early releases of the
11/1/24
Yoav Ben-Simon
,
Anthony Mathelier
2
11/1/24
Motif discovery in mutated/synthetic sequencs
Dear Yoav. You can use the TFBStools R bioconductor package. Best AM On Thursday, September 12, 2024
unread,
Motif discovery in mutated/synthetic sequencs
Dear Yoav. You can use the TFBStools R bioconductor package. Best AM On Thursday, September 12, 2024
11/1/24
Triana Forment
,
Anthony Mathelier
3
11/1/24
TF class / family classification
Dear Triana. You can get such a table using the pyJASPAR python module, the JASPAR2024 Bioconductor
unread,
TF class / family classification
Dear Triana. You can get such a table using the pyJASPAR python module, the JASPAR2024 Bioconductor
11/1/24
Ekaterina Khvatkova
,
Anthony Mathelier
3
11/1/24
MA1616.1 - Is It Mus Musculus or Homo Sapiens TFBS Data
Thanks for raising this issue. We will investigate and keep you posted. On Thursday, October 31, 2024
unread,
MA1616.1 - Is It Mus Musculus or Homo Sapiens TFBS Data
Thanks for raising this issue. We will investigate and keep you posted. On Thursday, October 31, 2024
11/1/24
Daniel Werbeblocker
,
Anthony Mathelier
2
8/16/24
JASPAR_2024_matrix_clustering_vertebrate
Thanks for raising this issue. Something is clearly wrong and we will try to fix as soon as possible.
unread,
JASPAR_2024_matrix_clustering_vertebrate
Thanks for raising this issue. Something is clearly wrong and we will try to fix as soon as possible.
8/16/24
Qiana Shin
,
Anthony Mathelier
5
7/9/24
scan for FASTA sequence
I found that it would work properly when I entered a longer FASTA sequence. Thank you for your help!
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scan for FASTA sequence
I found that it would work properly when I entered a longer FASTA sequence. Thank you for your help!
7/9/24
Tian Qiu
,
Anthony Mathelier
2
7/3/24
Zebrafish transpriction factor
Hi. The TF binding profiles are provided at the taxonomic group level; the species information are
unread,
Zebrafish transpriction factor
Hi. The TF binding profiles are provided at the taxonomic group level; the species information are
7/3/24
Marie-Odile BAUDEMENT
,
Anthony Mathelier
3
6/4/24
Find out some details on how the pairwise comparison of motifs has been created
Hi, Super, thank you for the link to the publication, I have started to explore it. I will contact
unread,
Find out some details on how the pairwise comparison of motifs has been created
Hi, Super, thank you for the link to the publication, I have started to explore it. I will contact
6/4/24
Vedran Franke
,
Anthony Mathelier
2
6/2/24
CTCFL binding motif
Dear Vedran. Thanks for your interest in JASPAR and your message. The CTCFL motif in JASPAR was
unread,
CTCFL binding motif
Dear Vedran. Thanks for your interest in JASPAR and your message. The CTCFL motif in JASPAR was
6/2/24
Charlie Hale
,
Anthony Mathelier
2
6/2/24
Using full CORE collection vs taxon-specific CORE collection
Dear Charlie. Thanks for your interest in JASPAR and for reaching out. You could theoretically run
unread,
Using full CORE collection vs taxon-specific CORE collection
Dear Charlie. Thanks for your interest in JASPAR and for reaching out. You could theoretically run
6/2/24
Gabriele Oliveto
,
Anthony Mathelier
2
4/9/24
Doubt regarding taxonomy
Dear Gabriele. Thanks for your inquiry. There is no link between the JASPAR IDs and the associated
unread,
Doubt regarding taxonomy
Dear Gabriele. Thanks for your inquiry. There is no link between the JASPAR IDs and the associated
4/9/24
Shang Su
,
Anthony Mathelier
2
4/9/24
How to interpret the different versions of JASPAR IDs for the same transcription factor?
Dear Shang. Thanks for your inquiry. We recommend users to use the newest version of each profile as
unread,
How to interpret the different versions of JASPAR IDs for the same transcription factor?
Dear Shang. Thanks for your inquiry. We recommend users to use the newest version of each profile as
4/9/24
Maggie Ma
,
Anthony Mathelier
2
4/9/24
Pseudocount
Dear Maggie. Thanks for reaching out. We do not use pseudocounts in the TF binding profiles stored in
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Pseudocount
Dear Maggie. Thanks for reaching out. We do not use pseudocounts in the TF binding profiles stored in
4/9/24
Yochay Tzur
,
Anthony Mathelier
2
4/9/24
Mouse TF motif points to human protein
Dear Yochay. Thanks for pointing that out. The issue here comes from the fact that the first version
unread,
Mouse TF motif points to human protein
Dear Yochay. Thanks for pointing that out. The issue here comes from the fact that the first version
4/9/24
Kelvin Ip
,
Anthony Mathelier
2
4/9/24
Can't find the source publication for the ChIP used for generating MA0535.1
Hi Kelvin. Unfortunately, it does not look like we have kept this information; the data has been
unread,
Can't find the source publication for the ChIP used for generating MA0535.1
Hi Kelvin. Unfortunately, it does not look like we have kept this information; the data has been
4/9/24
Brendan Rooney
, …
Anthony Mathelier
4
4/9/24
Confirming how to identify putative TF binding sites
Dear Gilles. Thanks for your interest in UniBind and your kind words. The TFBSs are indeed of high
unread,
Confirming how to identify putative TF binding sites
Dear Gilles. Thanks for your interest in UniBind and your kind words. The TFBSs are indeed of high
4/9/24