JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

被引：337

作者：

Rauluseviciute, Ieva ^{[1
]}

Riudavets-Puig, Rafael ^{[1
]}

Blanc-Mathieu, Romain ^{[2
]}

Castro-Mondragon, Jaime A. ^{[1
]}

Ferenc, Katalin ^{[1
]}

Kumar, Vipin ^{[1
]}

Lemma, Roza Berhanu ^{[1
]}

Lucas, Jeremy ^{[2
]}

Cheneby, Jeanne ^{[3
]}

Baranasic, Damir ^{[4
,5
,6
]}

Khan, Aziz ^{[7
]}

Fornes, Oriol ^{[8
]}

Gundersen, Sveinung

Johansen, Morten

Hovig, Eivind ^{[9
]}

Lenhard, Boris ^{[4
,5
]}

Sandelin, Albin ^{[10
,11
]}

Wasserman, Wyeth W. ^{[8
]}

Parcy, Francois ^{[2
]}

Mathelier, Anthony ^{[1
,3
,12
,13
]}

机构：

[1] Univ Oslo, Ctr Mol Med Norway NCMM, Nord EMBL Partnership, N-0318 Oslo, Norway

[2] Univ Grenoble Alpes, Lab Physiol Cellulaire & Vegetale, CNRS, CEA,INRAE,IRIG DBSCI LPCV, 17 Ave Martyrs, F-38054 Grenoble, France

[3] Univ Oslo, Ctr Bioinformat, Dept Informat, Oslo, Norway

[4] MRC London Inst Med Sci, Du Cane Rd, London W12 0NN, England

[5] Imperial Coll London, Hammersmith Hosp Campus, Inst Clin Sci, Fac Med, Du Cane Rd, London W12 0NN, England

[6] Rudjer Boskovic Inst, Div Elect, Zagreb 10000, Croatia

[7] Stanford Univ, Stanford Canc Inst, Sch Med, Stanford, CA 94305 USA

[8] Univ British Columbia, BC Childrens Hosp Res Inst, Ctr Mol Med & Therapeut, Dept Med Genet, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada

[9] Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0424 Oslo, Norway

[10] Univ Copenhagen, Dept Biol, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark

[11] Univ Copenhagen, Biotech Res & Innovat Ctr, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark

[12] Univ Oslo, Inst Clin Med, Dept Med Genet, Oslo, Norway

[13] Oslo Univ Hosp, Oslo, Norway

来源：

NUCLEIC ACIDS RESEARCH | 2023年 / 52卷 / D1期

基金：

英国医学研究理事会; 加拿大自然科学与工程研究理事会; 加拿大健康研究院;

关键词：

RNA-QUALITY-CONTROL; PROTEIN-BINDING; LINEAR MOTIFS; TRAMP COMPLEX; KINASE; PHOSPHORYLATION; ORGANIZATION; TERMINATION; ELIMINATION; EXOSOME;

D O I：

10.1093/nar/gkad1059

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Graphical Abstract

引用

页码：D174 / D182

页数：9

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