{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T17:09:44Z","timestamp":1774976984192,"version":"3.50.1"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,2,7]],"date-time":"2022-02-07T00:00:00Z","timestamp":1644192000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Shenzhen Key Medical Discipline Construction Fund","award":["SZXK045"],"award-info":[{"award-number":["SZXK045"]}]},{"name":"Shenzhen Key Laboratory of Prevention and Treatment of Severe Infections","award":["ZDSYS20200811142804014"],"award-info":[{"award-number":["ZDSYS20200811142804014"]}]},{"name":"Guangdong-Shenzhen Joint Fund of China","award":["2019A1515110097"],"award-info":[{"award-number":["2019A1515110097"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The advances in single-cell RNA sequencing (scRNA-seq) technologies enable the characterization of transcriptomic profiles at the cellular level and demonstrate great promise in bulk sample analysis thereby offering opportunities to transfer gene signature from scRNA-seq to bulk data. However, the gene expression signatures identified from single cells are typically inapplicable to bulk RNA-seq data due to the profiling differences of distinct sequencing technologies. Here, we propose single-cell pair-wise gene expression (scPAGE), a novel method to develop single-cell gene pair signatures (scGPSs) that were beneficial to bulk RNA-seq classification to transfer knowledge across platforms. PAGE was adopted to tackle the challenge of profiling differences. We applied the method to acute myeloid leukemia (AML) and identified the scGPS from mouse scRNA-seq that allowed discriminating between AML and control cells. The scGPS was validated in bulk RNA-seq datasets and demonstrated better performance (average area under the curve [AUC]\u2009=\u20090.96) than the conventional gene expression strategies (average AUC$\\le$\u00a00.88) suggesting its potential in disclosing the molecular mechanism of AML. The scGPS also outperformed its bulk counterpart, which highlighted the benefit of gene signature transfer. Furthermore, we confirmed the utility of scPAGE in sepsis as an example of other disease scenarios. scPAGE leveraged the advantages of single-cell profiles to enhance the analysis of bulk samples revealing great potential of transferring knowledge from single-cell to bulk transcriptome studies.<\/jats:p>","DOI":"10.1093\/bib\/bbac002","type":"journal-article","created":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T12:11:56Z","timestamp":1641384716000},"source":"Crossref","is-referenced-by-count":26,"title":["Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia"],"prefix":"10.1093","volume":"23","author":[{"given":"Ran","family":"Wang","sequence":"first","affiliation":[{"name":"Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China"},{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Xubin","family":"Zheng","sequence":"additional","affiliation":[{"name":"Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China"},{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China"}]},{"given":"Shibiao","family":"Wan","sequence":"additional","affiliation":[{"name":"Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA"}]},{"given":"Fangda","family":"Song","sequence":"additional","affiliation":[{"name":"School of Data Science, The Chinese University of Hong Kong, Shenzhen 518000, China"}]},{"given":"Man Hon","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"given":"Kwong Sak","family":"Leung","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9427-383X","authenticated-orcid":false,"given":"Lixin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, 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