{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:38:43Z","timestamp":1740184723209,"version":"3.37.3"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T00:00:00Z","timestamp":1634601600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Shanghai Municipal Science and Technology Project","award":["2017SHZDZX01","17DZ2203400","18430760500"],"award-info":[{"award-number":["2017SHZDZX01","17DZ2203400","18430760500"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22077079","81871448"],"award-info":[{"award-number":["22077079","81871448"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>High-dimensional mass cytometry (CyTOF), which provides both cellular signatures and inter-cluster interactions like the antagonism between immune activation and suppression, and the pro-inflammatory synergy, sheds light on the cellular and molecular basis of disease pathogenesis. However, revealing the aberrance of inter-cluster communication networks in CyTOF datasets remains a significant challenge.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we developed Sample Classification and direct Association Network among Cell clusters (SCANCell) that quantifies the direct association (DA) network of cell clusters. SCANCell was applied to profile inter-cluster interaction patterns of a well-recruited systemic lupus erythematosus (SLE) cohort, including 8 healthy controls, 10 active SLE patients (APs) and 8 remission SLE patients (RPs). SCANCell identified decreased inter-cluster interactions of CD8+ T cells in APs compared with RPs, and enhanced DA of CD8+ T cells after stimulation with immunostimulatory cytokine interleukin-2 in vitro. These discoveries prove that SCANCell can uncover pathology- and drug stimulation-associated inter-cluster interactions, which potentially benefits understanding of pathogenesis and novel therapeutic strategies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The main processing scripts of SCNACell are available at https:\/\/github.com\/Lxc417\/SCANCell. Other codes for the following data statistics are available from the corresponding author upon request.<\/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\/btab713","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T19:30:18Z","timestamp":1634153418000},"page":"1361-1368","source":"Crossref","is-referenced-by-count":1,"title":["SCANCell reveals diverse inter-cluster interaction patterns in systemic lupus erythematosus across the disease spectrum"],"prefix":"10.1093","volume":"38","author":[{"given":"Lulu","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University , Shanghai 200030, China"}]},{"given":"Xiao","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University , Shanghai 200030, China"}]},{"given":"Xiaoxiang","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Rheumatology, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital , Shanghai 200030, China"}]},{"given":"Antony R","family":"Warden","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University , Shanghai 200030, China"}]},{"given":"Youyi","family":"Yu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University , Shanghai 200030, China"}]},{"given":"Baozhen","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong , Hong Kong 999077, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1549-3499","authenticated-orcid":false,"given":"Xianting","family":"Ding","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University , Shanghai 200030, China"}]}],"member":"286","published-online":{"date-parts":[[2021,10,19]]},"reference":[{"key":"2023020108544199400_btab713-B2","doi-asserted-by":"crossref","first-page":"492","DOI":"10.3389\/fimmu.2017.00492","article-title":"An analysis of trafficking receptors shows that CD44 and P-selectin glycoprotein ligand-1 collectively control the migration of activated human T-cells","volume":"8","author":"Ali","year":"2017","journal-title":"Front. 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