{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:22:23Z","timestamp":1772173343059,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011971","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,11,4]],"date-time":"2024-11-04T00:00:00Z","timestamp":1730678400000}}],"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T00:00:00Z","timestamp":1729641600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003006","name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","doi-asserted-by":"publisher","award":["ETH-25 02-2"],"award-info":[{"award-number":["ETH-25 02-2"]}],"id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003006","name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","doi-asserted-by":"publisher","award":["23-2 ETH-015"],"award-info":[{"award-number":["23-2 ETH-015"]}],"id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (a chromVAR-limma workflow with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs\u2014in our case NFkB\u2014at the protein level.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011971","type":"journal-article","created":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T13:40:34Z","timestamp":1729690834000},"page":"e1011971","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["On the identification of differentially-active transcription factors from ATAC-seq data"],"prefix":"10.1371","volume":"20","author":[{"given":"Felix Ezequiel","family":"Gerbaldo","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4788-9508","authenticated-orcid":true,"given":"Emanuel","family":"Sonder","sequence":"additional","affiliation":[]},{"given":"Vincent","family":"Fischer","sequence":"additional","affiliation":[]},{"given":"Selina","family":"Frei","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6890-4732","authenticated-orcid":true,"given":"Jiayi","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Katharina","family":"Gapp","sequence":"additional","affiliation":[]},{"given":"Mark D.","family":"Robinson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3418-4218","authenticated-orcid":true,"given":"Pierre-Luc","family":"Germain","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2024,10,23]]},"reference":[{"issue":"19","key":"pcbi.1011971.ref001","doi-asserted-by":"crossref","first-page":"9557","DOI":"10.1093\/nar\/gks762","article-title":"Translation termination efficiency modulates ATF4 response by regulating ATF4 mRNA translation at 5\u2019 short ORFs","volume":"40","author":"H Ait Ghezala","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"31","key":"pcbi.1011971.ref002","doi-asserted-by":"crossref","first-page":"11269","DOI":"10.1073\/pnas.0400541101","article-title":"Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells","volume":"101","author":"KM Vattem","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"pcbi.1011971.ref003","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1093\/nar\/25.4.877","article-title":"Phosphorylation of ATF-1 enhances its DNA binding and transcription of the Na,K-ATPase alpha 1 subunit gene promoter","volume":"25","author":"M Kobayashi","year":"1997","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"pcbi.1011971.ref004","doi-asserted-by":"crossref","first-page":"a016709","DOI":"10.1101\/cshperspect.a016709","article-title":"Signaling by Nuclear Receptors","volume":"5","author":"R Sever","year":"2013","journal-title":"Cold Spring Harbor Perspectives in Biology"},{"issue":"12","key":"pcbi.1011971.ref005","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"JD Buenrostro","year":"2013","journal-title":"Nature Methods"},{"issue":"10","key":"pcbi.1011971.ref006","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nmeth.4396","article-title":"An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues","volume":"14","author":"MR Corces","year":"2017","journal-title":"Nature Methods"},{"issue":"7561","key":"pcbi.1011971.ref007","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14590","article-title":"Single-cell chromatin accessibility reveals principles of regulatory variation","volume":"523","author":"JD Buenrostro","year":"2015","journal-title":"Nature"},{"key":"pcbi.1011971.ref008","first-page":"060012","article-title":"Fast gene set enrichment analysis","author":"G Korotkevich","year":"2021","journal-title":"bioRxiv"},{"issue":"1","key":"pcbi.1011971.ref009","doi-asserted-by":"crossref","first-page":"vbac016","DOI":"10.1093\/bioadv\/vbac016","article-title":"decoupleR: ensemble of computational methods to infer biological activities from omics data","volume":"2","author":"IMP Badia","year":"2022","journal-title":"Bioinform Adv"},{"issue":"8","key":"pcbi.1011971.ref010","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/ng.3593","article-title":"Functional characterization of somatic mutations in cancer using network-based inference of protein activity","volume":"48","author":"MJ Alvarez","year":"2016","journal-title":"Nat Genet"},{"issue":"10","key":"pcbi.1011971.ref011","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1038\/nmeth.4401","article-title":"chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data","volume":"14","author":"AN Schep","year":"2017","journal-title":"Nat Methods"},{"issue":"9","key":"pcbi.1011971.ref012","doi-asserted-by":"crossref","first-page":"2624","DOI":"10.1093\/bioinformatics\/btac102","article-title":"monaLisa: an R\/Bioconductor package for identifying regulatory motifs","volume":"38","author":"D Machlab","year":"2022","journal-title":"Bioinformatics"},{"issue":"10","key":"pcbi.1011971.ref013","doi-asserted-by":"crossref","first-page":"3147","DOI":"10.1016\/j.celrep.2019.10.106","article-title":"Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF","volume":"29","author":"I Berest","year":"2019","journal-title":"Cell Rep"},{"issue":"8","key":"pcbi.1011971.ref014","doi-asserted-by":"crossref","first-page":"1710","DOI":"10.1016\/j.celrep.2017.05.003","article-title":"Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity","volume":"19","author":"S Baek","year":"2017","journal-title":"Cell Rep"},{"issue":"9","key":"pcbi.1011971.ref015","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.1101\/gr.233346.117","article-title":"Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding","volume":"28","author":"IC McDowell","year":"2018","journal-title":"Genome Research"},{"issue":"4","key":"pcbi.1011971.ref016","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1016\/j.cell.2019.06.026","article-title":"Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility","volume":"178","author":"J Guan","year":"2019","journal-title":"Cell"},{"key":"pcbi.1011971.ref017","doi-asserted-by":"crossref","first-page":"101291","DOI":"10.1016\/j.molmet.2021.101291","article-title":"Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRalpha","volume":"53","author":"J Kain","year":"2021","journal-title":"Mol Metab"},{"issue":"1","key":"pcbi.1011971.ref018","doi-asserted-by":"crossref","first-page":"2969","DOI":"10.1038\/s41467-021-23213-w","article-title":"High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer","volume":"12","author":"SE Pierce","year":"2021","journal-title":"Nat Commun"},{"issue":"7870","key":"pcbi.1011971.ref019","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/s41586-021-03689-8","article-title":"BANP opens chromatin and activates CpG-island-regulated genes","volume":"596","author":"RS Grand","year":"2021","journal-title":"Nature"},{"issue":"15","key":"pcbi.1011971.ref020","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"4","key":"pcbi.1011971.ref021","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nature Methods"},{"issue":"1","key":"pcbi.1011971.ref022","doi-asserted-by":"crossref","first-page":"9354","DOI":"10.1038\/s41598-019-45839-z","article-title":"The ENCODE Blacklist: Identification of Problematic Regions of the Genome","volume":"9","author":"HM Amemiya","year":"2019","journal-title":"Scientific Reports"},{"issue":"1","key":"pcbi.1011971.ref023","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"pcbi.1011971.ref024","doi-asserted-by":"crossref","first-page":"D252","DOI":"10.1093\/nar\/gkx1106","article-title":"HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis","volume":"46","author":"IV Kulakovskiy","year":"2018","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1011971.ref025","article-title":"MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs","author":"P Shannon","year":"2020","journal-title":"Bioconductor"},{"issue":"7","key":"pcbi.1011971.ref026","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: scanning for occurrences of a given motif","volume":"27","author":"CE Grant","year":"2011","journal-title":"Bioinformatics"},{"issue":"7818","key":"pcbi.1011971.ref027","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1038\/s41586-020-2528-x","article-title":"Global reference mapping of human transcription factor footprints","volume":"583","author":"J Vierstra","year":"2020","journal-title":"Nature"},{"issue":"7","key":"pcbi.1011971.ref028","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"ME Ritchie","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"pcbi.1011971.ref029","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities","volume":"38","author":"S Heinz","year":"2010","journal-title":"Molecular Cell"},{"issue":"3","key":"pcbi.1011971.ref030","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1016\/j.ajhg.2019.01.002","article-title":"ACAT: A Fast and Powerful p Value Combination Method for Rare-Variant Analysis in Sequencing Studies","volume":"104","author":"Y Liu","year":"2019","journal-title":"The American Journal of Human Genetics"},{"key":"pcbi.1011971.ref031","article-title":"Transcription factor activities enhance markers of drug sensitivity in cancer","author":"LM Garcia-Alonso","year":"2017","journal-title":"Cancer Research"},{"key":"pcbi.1011971.ref032","unstructured":"Ou J. ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq. Bioconductor. 2023;."},{"issue":"2","key":"pcbi.1011971.ref033","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/j.molcel.2014.08.016","article-title":"DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence","volume":"56","author":"MH Sung","year":"2014","journal-title":"Molecular Cell"},{"issue":"1","key":"pcbi.1011971.ref034","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1186\/s12859-020-03739-4","article-title":"MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates","volume":"21","author":"NP Delos Santos","year":"2020","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pcbi.1011971.ref035","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society: Series B (Methodological)"},{"issue":"7414","key":"pcbi.1011971.ref036","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"The ENCODE Consortium","year":"2012","journal-title":"Nature"},{"issue":"6","key":"pcbi.1011971.ref037","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"issue":"6","key":"pcbi.1011971.ref038","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/j.ajhg.2017.05.006","article-title":"YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction","volume":"100","author":"M Gabriele","year":"2017","journal-title":"The American Journal of Human Genetics"},{"issue":"5","key":"pcbi.1011971.ref039","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.chembiol.2021.03.011","article-title":"Targeted degradation of transcription factors by TRAFTACs: TRAnscription Factor TArgeting Chimeras","volume":"28","author":"KTG Samarasinghe","year":"2021","journal-title":"Cell Chemical Biology"},{"issue":"3","key":"pcbi.1011971.ref040","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"MD Robinson","year":"2010","journal-title":"Genome Biology"},{"issue":"11","key":"pcbi.1011971.ref041","doi-asserted-by":"crossref","first-page":"100321","DOI":"10.1016\/j.crmeth.2022.100321","article-title":"Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects","volume":"2","author":"K Van Den Berge","year":"2022","journal-title":"Cell Reports Methods"},{"issue":"8","key":"pcbi.1011971.ref042","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1016\/j.chembiol.2020.07.020","article-title":"PROTACs: An Emerging Therapeutic Modality in Precision Medicine","volume":"27","author":"DA Nalawansha","year":"2020","journal-title":"Cell Chemical Biology"},{"issue":"3","key":"pcbi.1011971.ref043","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.smim.2014.02.009","article-title":"TNF and MAP kinase signalling pathways","volume":"26","author":"G Sabio","year":"2014","journal-title":"Seminars in Immunology"},{"issue":"10","key":"pcbi.1011971.ref044","doi-asserted-by":"crossref","first-page":"4209","DOI":"10.1182\/blood-2005-09-031963","article-title":"Modulation of DNA binding properties of CCAAT\/enhancer binding protein epsilon by heterodimer formation and interactions with NFkappaB pathway","volume":"109","author":"AM Chumakov","year":"2007","journal-title":"Blood"},{"issue":"0","key":"pcbi.1011971.ref045","article-title":"Benchmarking tools for transcription factor prioritization","volume":"0","author":"LS Santana","year":"2024","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"pcbi.1011971.ref046","doi-asserted-by":"crossref","first-page":"W212","DOI":"10.1093\/nar\/gkz446","article-title":"ChEA3: transcription factor enrichment analysis by orthogonal omics integration","volume":"47","author":"AB Keenan","year":"2019","journal-title":"Nucleic Acids Research"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1011971","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,11,4]],"date-time":"2024-11-04T00:00:00Z","timestamp":1730678400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011971","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,4]],"date-time":"2024-11-04T13:42:26Z","timestamp":1730727746000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011971"}},"subtitle":[],"editor":[{"given":"Shaun","family":"Mahony","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,10,23]]},"references-count":46,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2024,10,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1011971","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.03.06.583825","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,23]]}}}