Regarding the Update and Changes of Gene Information for the Lyl1 Gene in the JASPAR Database
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jackhao lin
Jun 27, 2025, 5:38:06 AMJun 27
to JASPAR Q&A Forum
Dear JASPAR Team,
I hope this message finds you well.
I would like to inquire about a matter and hope to receive a response. In August 2023, we found relevant information regarding the mouse Lyl1 gene through JASPAR, and we used this information to predict its binding to the upstream sequences of several genes. However, in the 2024 version, we could not find any related information or genes concerning Lyl1. I would appreciate it if you could inform us of the reason for the removal of this information.
Attached is an image showing the prediction of Lyl1 binding to specific gene upstream sequences that we conducted during 2023.
Thank you for your assistance!
Anthony Mathelier
Jun 30, 2025, 2:49:12 AMJun 30
to jackhao lin, JASPAR Q&A Forum
Dear Jackhao Lin.
Thanks for reaching out.
The 2022 release of JASPAR indeed contained a profile for Lyl1, but note that this profile was part of the UNVALIDATED collection. As provided on our webpage: "These profiles are regarded as unvalidated because our curators failed to find any orthogonal support from existing literature. We encourage the community to perform experiments and/or point us to literature that our curators missed in order to support these profiles."
After further manual curation, we removed this profile for the JASPAR 2024 release since it does not match the expected bHLH motif. The profile was derived from ChIP-seq and likely corresponds to a false positive motif or a motif bound by another factor. This profile is also contained in HOCOMOCO but evaluated as of poor quality (https://hocomoco13.autosome.org/motif/LYL1.H13CORE.1.P.C#mainInfo).
I hope that helps.
Best
AM
Thanks for reaching out.
The 2022 release of JASPAR indeed contained a profile for Lyl1, but note that this profile was part of the UNVALIDATED collection. As provided on our webpage: "These profiles are regarded as unvalidated because our curators failed to find any orthogonal support from existing literature. We encourage the community to perform experiments and/or point us to literature that our curators missed in order to support these profiles."
After further manual curation, we removed this profile for the JASPAR 2024 release since it does not match the expected bHLH motif. The profile was derived from ChIP-seq and likely corresponds to a false positive motif or a motif bound by another factor. This profile is also contained in HOCOMOCO but evaluated as of poor quality (https://hocomoco13.autosome.org/motif/LYL1.H13CORE.1.P.C#mainInfo).
I hope that helps.
Best
AM
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