{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T09:57:17Z","timestamp":1773827837423,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T00:00:00Z","timestamp":1604275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2018M3C9A5064705"],"award-info":[{"award-number":["NRF-2018M3C9A5064705"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2015K1A4A3047851"],"award-info":[{"award-number":["NRF-2015K1A4A3047851"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2014M3C9A3065221"],"award-info":[{"award-number":["NRF-2014M3C9A3065221"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003715","name":"Korea Research Institute of Bioscience and Biotechnology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003715","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>High-throughput screening based on CRISPR-Cas9 libraries has become an attractive and powerful technique to identify target genes for functional studies. However, accessibility of public data is limited due to the lack of user-friendly utilities and up-to-date resources covering experiments from third parties. Here, we describe iCSDB, an integrated database of CRISPR screening experiments using human cell lines. We compiled two major sources of CRISPR-Cas9 screening: the DepMap portal and BioGRID ORCS. DepMap portal itself is an integrated database that includes three large-scale projects of CRISPR screening. We additionally aggregated CRISPR screens from BioGRID ORCS that is a collection of screening results from PubMed articles. Currently, iCSDB contains 1375 genome-wide screens across 976 human cell lines, covering 28 tissues and 70 cancer types. Importantly, the batch effects from different CRISPR libraries were removed and the screening scores were converted into a single metric to estimate the knockout efficiency. Clinical and molecular information were also integrated to help users to select cell lines of interest readily. Furthermore, we have implemented various interactive tools and viewers to facilitate users to choose, examine and compare the screen results both at the gene and guide RNA levels. iCSDB is available at https:\/\/www.kobic.re.kr\/icsdb\/.<\/jats:p>","DOI":"10.1093\/nar\/gkaa989","type":"journal-article","created":{"date-parts":[[2020,10,13]],"date-time":"2020-10-13T12:32:32Z","timestamp":1602592352000},"page":"D956-D961","source":"Crossref","is-referenced-by-count":24,"title":["iCSDB: an integrated database of CRISPR screens"],"prefix":"10.1093","volume":"49","author":[{"given":"Ahyoung","family":"Choi","sequence":"first","affiliation":[{"name":"Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea"}]},{"given":"Insu","family":"Jang","sequence":"additional","affiliation":[{"name":"Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea"}]},{"given":"Heewon","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea"}]},{"given":"Min-Seo","family":"Kim","sequence":"additional","affiliation":[{"name":"Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea"}]},{"given":"Jinhyuk","family":"Choi","sequence":"additional","affiliation":[{"name":"Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea"}]},{"given":"Jieun","family":"Lee","sequence":"additional","affiliation":[{"name":"Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul 03760, Republic of Korea"}]},{"given":"Sung-Yup","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea"}]},{"given":"Yukyung","family":"Jun","sequence":"additional","affiliation":[{"name":"Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul 03760, Republic of Korea"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington,\u00a0CT 06032, U.S.A"}]},{"given":"Charles","family":"Lee","sequence":"additional","affiliation":[{"name":"Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul 03760, Republic of Korea"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington,\u00a0CT 06032, U.S.A"},{"name":"Precision Medicine Center, The First Affiliated Hospital of Xi\u2019an Jiaotong University, Xi\u2019an 710061, People\u2019s Republic of China"}]},{"given":"Jaesang","family":"Kim","sequence":"additional","affiliation":[{"name":"Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul 03760, Republic of Korea"},{"name":"Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea"}]},{"given":"Byungwook","family":"Lee","sequence":"additional","affiliation":[{"name":"Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9230-7461","authenticated-orcid":false,"given":"Sanghyuk","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea"},{"name":"Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul 03760, Republic of Korea"},{"name":"Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea"}]}],"member":"286","published-online":{"date-parts":[[2020,11,2]]},"reference":[{"key":"2021010313110799400_B1","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1038\/nrg1836","article-title":"High-throughput RNAi screening in cultured cells: a user's guide","volume":"7","author":"Echeverri","year":"2006","journal-title":"Nat. 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Syst. Biol."},{"key":"2021010313110799400_B6","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1146\/annurev-biochem-060815-014607","article-title":"CRISPR\/Cas9 in genome editing and beyond","volume":"85","author":"Wang","year":"2016","journal-title":"Annu. Rev. Biochem."},{"key":"2021010313110799400_B7","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/s41586-019-1103-9","article-title":"Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens","volume":"568","author":"Behan","year":"2019","journal-title":"Nature"},{"key":"2021010313110799400_B8","doi-asserted-by":"crossref","first-page":"5817","DOI":"10.1038\/s41467-019-13805-y","article-title":"Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets","volume":"10","author":"Dempster","year":"2019","journal-title":"Nat. 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