{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T20:07:41Z","timestamp":1779912461849,"version":"3.53.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T00:00:00Z","timestamp":1779840000000},"content-version":"vor","delay-in-days":26,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Expression quantitative trait locus (eQTL) mapping is used to identify the functional link between a genomic variant and a gene\u2019s expression. A significant eQTL association does not mean a causal relationship or mechanism, and further investigation is needed to understand how a single-nucleotide polymorphism (SNP) impacts gene expression. One of the most plausible explanations for eQTL is that a genomic variant affects transcription factor (TF) binding and thus impacts its regulation on target genes (TGs). However, the current eQTL model does not provide information on the TF and how its regulation is mediated by the SNP\u2019s genotypes. Here, we propose a new method called differential co-expression QTL (ceQTL) among different alleles using Chow statistics to specifically detect eQTLs that are bound by a particular TF. We start with building a trio of TF, its TG, and related SNP, and then test the significant coefficient difference among different genotypes of the SNP. We applied this ceQTL model to simulated data and the lung tissue datasets from the genotype-tissue expression project. The simulated data results showed that the model was robust to detect true ceQTLs at variable sample sizes and different minor allele frequencies as measured by area under the curve. Our tool also performed a TF binding affinity analysis to add another layer of evidence for functional interpretation. In summary, ceQTL analysis provides a more interpretable and biological insight into the mechanism of eQTL and transcriptomic regulation, which would help us better understand how genomic variants affect phenotypes and diseases.<\/jats:p>","DOI":"10.1093\/bib\/bbag258","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T11:27:28Z","timestamp":1777980448000},"source":"Crossref","is-referenced-by-count":0,"title":["ceQTL: a co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation"],"prefix":"10.1093","volume":"27","author":[{"given":"Panwen","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Quantitative Health Sciences, Mayo Clinic , Scottsdale, AZ 85259 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanxi","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Mayo Clinic , Scottsdale, AZ 85259 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Mayo Clinic , Scottsdale, AZ 85259 ,","place":["United States"]},{"name":"College of Electronic Information, Guangxi Minzu University, 188 East University Road , Nanning, Guangxi 530006 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4002-7497","authenticated-orcid":false,"given":"Li","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Health Solutions, Arizona State University , Phoenix, AZ 85004 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8588-847X","authenticated-orcid":false,"given":"Ping","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Mayo Clinic , Scottsdale, AZ 85259 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4432-4707","authenticated-orcid":false,"given":"Junwen","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Mayo Clinic , Scottsdale, AZ 85259 ,","place":["United States"]},{"name":"Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong , Hong Kong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhifu","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Mayo Clinic , Rochester, MN 55905 ,","place":["United 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