{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T09:06:46Z","timestamp":1768554406185,"version":"3.49.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,26]],"date-time":"2019-08-26T00:00:00Z","timestamp":1566777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"The National Key Plan for Scientific Research and Development of China","award":["2016YFD0500301"],"award-info":[{"award-number":["2016YFD0500301"]}]},{"name":"The CAMS Initiative for Innovative Medicine","award":["2016-I2M-1-005"],"award-info":[{"award-number":["2016-I2M-1-005"]}]},{"name":"Six-talent Peaks Project in the Jiangsu Province","award":["SWYY-169"],"award-info":[{"award-number":["SWYY-169"]}]},{"name":"The Jiangsu Provincial Natural Science Foundation","award":["BK20161245"],"award-info":[{"award-number":["BK20161245"]}]},{"name":"The Open Project Program of the National Laboratory of Pattern Recognition","award":["201900004"],"award-info":[{"award-number":["201900004"]}]},{"name":"The Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences","award":["2018RC310022"],"award-info":[{"award-number":["2018RC310022"]}]},{"name":"Central Public-Interest Scientific Institution Basal Research Fund","award":["2016ZX310195"],"award-info":[{"award-number":["2016ZX310195"]}]},{"name":"Central Public-Interest Scientific Institution Basal Research Fund","award":["2017PT31026"],"award-info":[{"award-number":["2017PT31026"]}]},{"name":"Central Public-Interest Scientific Institution Basal Research Fund","award":["2018PT31016"],"award-info":[{"award-number":["2018PT31016"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Many methods have been developed to estimate immune cell composition from tissue transcriptomes. One common characteristic of these methods is that they are trained using a set of general immune cell transcriptomes that ignores tissue specificities. However, as immune cells are localized in different tissues, they may have distinct expression profiles. Hence, calculations that use general signature matrices may hinder the deconvolution accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This study used single cell RNA-sequencing (scRNA-Seq) data from different mouse tissues instead of general signature expression values to generate tissue-specific signature gene matrices that are used as the input of the deconvolution model. First, the transcriptome of immune cells in each tissue was extracted from scRNA-Seq data and used to construct the entire expression matrix of tissue immune cells. Then, after comparing different gene selection strategies, the expressions of 162 seq-ImmuCC derived signature genes in tissue immune cell scRNA-Seq data were regarded as the tissue specific signature matrices. Finally, a modest improvement in performance was observed in multiple tissues that refer to a traditional general signature matrix in the deconvolution model. With the fast accumulation of scRNA-Seq data, the introduction of these data into an estimation of immune cell compositions for different tissues will open a new window for avoiding tissue bias for immune cell expression.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The signature matrices were available at https:\/\/github.com\/wuaipinglab\/ImmuCC\/tree\/master\/tissue_immucc\/SignatureMatrix).<\/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\/btz672","type":"journal-article","created":{"date-parts":[[2019,8,22]],"date-time":"2019-08-22T12:13:39Z","timestamp":1566476019000},"page":"819-827","source":"Crossref","is-referenced-by-count":18,"title":["Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes"],"prefix":"10.1093","volume":"36","author":[{"given":"Ziyi","family":"Chen","sequence":"first","affiliation":[{"name":"Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou Institute of Systems Medicine , Suzhou 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengyang","family":"Ji","sequence":"additional","affiliation":[{"name":"Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou Institute of Systems Medicine , Suzhou 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qin","family":"Shen","sequence":"additional","affiliation":[{"name":"Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou Institute of Systems Medicine , Suzhou 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou Institute of Systems Medicine , Suzhou 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F Xiao-Feng","family":"Qin","sequence":"additional","affiliation":[{"name":"Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou Institute of Systems Medicine , Suzhou 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aiping","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100005, China"},{"name":"Suzhou Institute of Systems Medicine , Suzhou 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,8,26]]},"reference":[{"key":"2023013110024473600_btz672-B1","doi-asserted-by":"crossref","first-page":"e6098.","DOI":"10.1371\/journal.pone.0006098","article-title":"Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus","volume":"4","author":"Abbas","year":"2009","journal-title":"PLoS One"},{"key":"2023013110024473600_btz672-B2","doi-asserted-by":"crossref","first-page":"720.","DOI":"10.1002\/msb.134947","article-title":"Digital cell quantification identifies global immune cell dynamics during influenza infection","volume":"10","author":"Altboum","year":"2014","journal-title":"Mol. 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