{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:11Z","timestamp":1772138471376,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,11]],"date-time":"2024-01-11T00:00:00Z","timestamp":1704931200000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM130564"],"award-info":[{"award-number":["R01GM130564"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Altered open chromatin regions, impacting gene expression, is a feature of some human disorders. We discovered it is possible to detect global changes in genomically-related adjacent gene co-expression within single cell RNA sequencing (scRNA-seq) data. We built a software package to generate and test non-randomness using \u2018Brooklyn plots\u2019 to identify the percent of genes significantly co-expressed from the same chromosome in \u223c10\u00a0MB intervals across the genome. These plots establish an expected low baseline of co-expression in scRNA-seq from most cell types, but, as seen in dilated cardiomyopathy cardiomyocytes, altered patterns of open chromatin appear. These may relate to larger regions of transcriptional bursting, observable in single cell, but not bulk datasets.<\/jats:p>","DOI":"10.1093\/nargab\/lqad112","type":"journal-article","created":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T11:58:05Z","timestamp":1703073485000},"source":"Crossref","is-referenced-by-count":0,"title":["Brooklyn plots to identify co-expression dysregulation in single cell sequencing"],"prefix":"10.1093","volume":"6","author":[{"given":"Arun H","family":"Patil","sequence":"first","affiliation":[{"name":"Lieber Institute for Brain Development , Baltimore , MD , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew N","family":"McCall","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Computational Biology, University of Rochester Medical Center , Rochester , NY , USA"},{"name":"Department of Biomedical Genetics, University of Rochester Medical Center , Rochester , NY , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7112-7389","authenticated-orcid":false,"given":"Marc K","family":"Halushka","sequence":"additional","affiliation":[{"name":"Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation , Cleveland , OH , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,1,11]]},"reference":[{"key":"2024032810404903800_B1","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1038\/s41556-021-00787-7","article-title":"Cell type ontologies of the Human Cell Atlas","volume":"23","author":"Osumi-Sutherland","year":"2021","journal-title":"Nat. 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