{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:05Z","timestamp":1740185105108,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T00:00:00Z","timestamp":1634774400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","award":["R00AR065480","R01AR075015"],"award-info":[{"award-number":["R00AR065480","R01AR075015"]}],"id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Scholar","award":["RSG-21-018-01-DDC"],"award-info":[{"award-number":["RSG-21-018-01-DDC"]}]},{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Searle Leadership Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Eukaryotic gene expression requires coordination among hundreds of transcriptional regulators. To characterize a specific transcriptional regulator, identifying how it shares genomic-binding sites with other regulators can generate important insights into its action. As genomic data such as chromatin immunoprecipitation assays with sequencing (ChIP-Seq) are being continously generated from individual labs, there is a demand for timely integration and analysis of these new data. We have developed an R package, GPSmatch (Genomic-binding Profile Similarity match), for calculating the Jaccard index to compare the ChIP-Seq peaks from one experiment to other experiments stored in a user-supplied customizable database. GPSmatch also evaluates the statistical significance of the calculated Jaccard index using a nonparametric Monte Carlo procedure. We show that GPSmatch is suitable for identifying and ranking transcriptional regulators with shared genomic-binding profiles, which may unravel potential mechanistic actions of gene regulation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software is freely available at https:\/\/github.com\/Bao-Lab\/GPSmatch.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab728","type":"journal-article","created":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T11:52:20Z","timestamp":1634644340000},"page":"853-855","source":"Crossref","is-referenced-by-count":0,"title":["GPSmatch: an R package for comparing Genomic-binding Profile Similarity among transcriptional regulators using customizable databases"],"prefix":"10.1093","volume":"38","author":[{"given":"Amy","family":"Dong","sequence":"first","affiliation":[{"name":"Hinsdale Central High School , Hinsdale, IL 60521, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8845-5012","authenticated-orcid":false,"given":"Xiaomin","family":"Bao","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, Northwestern University , Evanston, IL 60208, USA"},{"name":"Department of Dermatology, Northwestern University , Chicago, IL 60611, USA"},{"name":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University , Chicago, IL 60611, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,10,21]]},"reference":[{"volume-title":"Computational Genomics with R","year":"2021","author":"Akalin","key":"2023020108502371200_btab728-B1"},{"key":"2023020108502371200_btab728-B2","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1186\/s13059-015-0840-9","article-title":"A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63","volume":"16","author":"Bao","year":"2015","journal-title":"Genome Biol"},{"key":"2023020108502371200_btab728-B3","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","year":"2012","journal-title":"Nature"},{"key":"2023020108502371200_btab728-B4","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1038\/s41588-018-0102-3","article-title":"Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity","volume":"50","author":"Harley","year":"2018","journal-title":"Nat. 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