{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T09:22:34Z","timestamp":1775640154008,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01LM012806"],"award-info":[{"award-number":["R01LM012806"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01DE030122"],"award-info":[{"award-number":["R01DE030122"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01DE029818"],"award-info":[{"award-number":["R01DE029818"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["RP180734"],"award-info":[{"award-number":["RP180734"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["RP210045"],"award-info":[{"award-number":["RP210045"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Gulf Coast Consortia on Training in Precision Environmental Health Sciences","award":["T32ES027801"],"award-info":[{"award-number":["T32ES027801"]}]},{"DOI":"10.13039\/100000092","name":"National Library of Medicine","doi-asserted-by":"publisher","award":["T15LM007093"],"award-info":[{"award-number":["T15LM007093"]}],"id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Human complex traits and common diseases show tissue- and cell-type- specificity. Recently, single-cell RNA sequencing (scRNA-seq) technology has successfully depicted cellular heterogeneity in human tissue, providing an unprecedented opportunity to understand the context-specific expression of complex trait-associated genes in human tissue-cell types (TCs). Here, we present the first web-based application to quickly assess the cell-type-specificity of genes, named Web-based Cell-type Specific Enrichment Analysis of Genes (WebCSEA, available at https:\/\/bioinfo.uth.edu\/webcsea\/). Specifically, we curated a total of 111 scRNA-seq panels of human tissues and 1,355 TCs from 61 different general tissues across 11 human organ systems. We adapted our previous decoding tissue-specificity (deTS) algorithm to measure the enrichment for each tissue-cell type (TC). To overcome the potential bias from the number of signature genes between different TCs, we further developed a permutation-based method that accurately estimates the TC-specificity of a given inquiry gene list. WebCSEA also provides an interactive heatmap that displays the cell-type specificity across 1355 human TCs, and other interactive and static visualizations of cell-type specificity by human organ system, developmental stage, and top-ranked tissues and cell types. In short, WebCSEA is a one-click application that provides a comprehensive exploration of the TC-specificity of genes among human major TC map.<\/jats:p>","DOI":"10.1093\/nar\/gkac392","type":"journal-article","created":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T11:17:16Z","timestamp":1651749436000},"page":"W782-W790","source":"Crossref","is-referenced-by-count":117,"title":["WebCSEA: web-based cell-type-specific enrichment analysis of genes"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1874-7893","authenticated-orcid":false,"given":"Yulin","family":"Dai","sequence":"first","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5549-3082","authenticated-orcid":false,"given":"Ruifeng","family":"Hu","sequence":"additional","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"},{"name":"Center for Advanced Parkinson Research, Brigham and Women's Hospital, Harvard Medical School , Boston , MA 02115 , USA"},{"name":"Genomics and Bioinformatics Hub, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School , Boston , MA 02115 , USA"}]},{"given":"Andi","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"},{"name":"Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"}]},{"given":"Kyung Serk","family":"Cho","sequence":"additional","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"}]},{"given":"Astrid Marilyn","family":"Manuel","sequence":"additional","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"}]},{"given":"Xiaoyang","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"},{"name":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8052-9320","authenticated-orcid":false,"given":"Xianjun","family":"Dong","sequence":"additional","affiliation":[{"name":"Center for Advanced Parkinson Research, Brigham and Women's Hospital, Harvard Medical School , Boston , MA 02115 , USA"},{"name":"Genomics and Bioinformatics Hub, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School , Boston , MA 02115 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4523-4153","authenticated-orcid":false,"given":"Peilin","family":"Jia","sequence":"additional","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3477-0914","authenticated-orcid":false,"given":"Zhongming","family":"Zhao","sequence":"additional","affiliation":[{"name":"Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston , TX 77030 , USA"},{"name":"MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences , Houston , TX 77030 , USA"}]}],"member":"286","published-online":{"date-parts":[[2022,5,24]]},"reference":[{"key":"2023072021471960600_B1","doi-asserted-by":"crossref","first-page":"e27041","DOI":"10.7554\/eLife.27041","article-title":"The human cell atlas","volume":"6","author":"Regev","year":"2017","journal-title":"Elife"},{"key":"2023072021471960600_B2","doi-asserted-by":"crossref","first-page":"eabl4896","DOI":"10.1126\/science.abl4896","article-title":"The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans","volume":"376","author":"Jones","year":"2022","journal-title":"Science"},{"key":"2023072021471960600_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1906-x","article-title":"scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation","volume":"21","author":"Madissoon","year":"2019","journal-title":"Genome 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