JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
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JASPAR 2024 : 20th anniversary of the open-access database of transcription factor binding profiles. / Rauluseviciute, Ieva; Riudavets-puig, Rafael; Blanc-mathieu, Romain; Castro-mondragon, Jaime a; Ferenc, Katalin; Kumar, Vipin; Lemma, Roza Berhanu; Lucas, Jérémy; Chèneby, Jeanne; Baranasic, Damir; Khan, Aziz; Fornes, Oriol; Gundersen, Sveinung; Johansen, Morten; Hovig, Eivind; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth w; Parcy, François; Mathelier, Anthony.
In: Nucleic Acids Symposium Series, Vol. 52, No. D1, 2024, p. D174–D182.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - JASPAR 2024
T2 - 20th anniversary of the open-access database of transcription factor binding profiles
AU - Rauluseviciute, Ieva
AU - Riudavets-puig, Rafael
AU - Blanc-mathieu, Romain
AU - Castro-mondragon, Jaime a
AU - Ferenc, Katalin
AU - Kumar, Vipin
AU - Lemma, Roza Berhanu
AU - Lucas, Jérémy
AU - Chèneby, Jeanne
AU - Baranasic, Damir
AU - Khan, Aziz
AU - Fornes, Oriol
AU - Gundersen, Sveinung
AU - Johansen, Morten
AU - Hovig, Eivind
AU - Lenhard, Boris
AU - Sandelin, Albin
AU - Wasserman, Wyeth w
AU - Parcy, François
AU - Mathelier, Anthony
PY - 2024
Y1 - 2024
N2 - JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
AB - JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
U2 - 10.1093/nar/gkad1059
DO - 10.1093/nar/gkad1059
M3 - Journal article
C2 - 37962376
VL - 52
SP - D174–D182
JO - Nucleic acids symposium series
JF - Nucleic acids symposium series
SN - 0261-3166
IS - D1
ER -
ID: 375299725