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Biol."],"published-print":{"date-parts":[[2020,9]]},"abstract":"<jats:p>The Cistrome Data Browser (DB) at the website (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/cistrome.org\/db\">cistrome.org\/db<\/jats:ext-link>) provides about 56,000 published human and mouse ChIP\u2010seq, DNase\u2010seq, and ATAC\u2010seq chromatin profiles, which we have processed using uniform analysis and quality control pipelines. The Cistrome DB Toolkit at the website (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/dbtoolkit.cistrome.org\">dbtoolkit.cistrome.org<\/jats:ext-link>) was developed to allow users to investigate fundamental questions using this data collection. In this tutorial, we describe how to use the Cistrome DB to search for publicly available chromatin profiles, to assess sample quality, to access peak results, to visualize signal intensities, to explore DNA sequence motifs, and to identify putative target genes. We also describe the use of the Toolkit module to seek the factors most likely to regulate a gene of interest, the factors that bind to a given genomic interval (enhancer, SNP, etc.), and samples that have significant peak overlaps with user\u2010defined peak sets. This tutorial guides biomedical researchers in the use of Cistrome DB resources to rapidly obtain valuable insights into gene regulatory questions<\/jats:p>","DOI":"10.1007\/s40484-020-0204-7","type":"journal-article","created":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T04:26:57Z","timestamp":1588652817000},"page":"267-276","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP\u2010seq and chromatin accessibility data"],"prefix":"10.1002","volume":"8","author":[{"given":"Rongbin","family":"Zheng","sequence":"first","affiliation":[{"name":"<!--1--> Clinical Translational Research Center Shanghai Pulmonary Hospital School of Life Science and Technology Tongji University Shanghai 200433 China"},{"name":"<!--2--> Department of Bioinformatics School of Life Science and Technology Tongji University Shanghai 200092 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Dong","sequence":"additional","affiliation":[{"name":"<!--1--> Clinical Translational Research Center Shanghai Pulmonary Hospital School of Life Science and Technology Tongji University Shanghai 200433 China"},{"name":"<!--2--> Department of Bioinformatics School of Life Science and Technology Tongji University Shanghai 200092 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Changxin","family":"Wan","sequence":"additional","affiliation":[{"name":"<!--1--> Clinical Translational Research Center Shanghai Pulmonary Hospital School of Life Science and Technology Tongji University Shanghai 200433 China"},{"name":"<!--2--> Department of Bioinformatics School of Life Science and Technology Tongji University Shanghai 200092 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoying","family":"Shi","sequence":"additional","affiliation":[{"name":"<!--1--> Clinical Translational Research Center Shanghai Pulmonary Hospital School of Life Science and Technology Tongji University Shanghai 200433 China"},{"name":"<!--2--> Department of Bioinformatics School of Life Science and Technology Tongji University Shanghai 200092 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyan","family":"Zhang","sequence":"additional","affiliation":[{"name":"<!--2--> Department of Bioinformatics School of Life Science and Technology Tongji University Shanghai 200092 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clifford A.","family":"Meyer","sequence":"additional","affiliation":[{"name":"<!--3--> Department of Data Science Dana\u2010Farber Cancer Institute and Harvard T.H. Chan School of Public Health Boston MA 02215 USA"},{"name":"<!--4--> Center for Functional Cancer Epigenetics Dana\u2010Farber Cancer Institute Boston MA 02215 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2020,9]]},"reference":[{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1141319"},{"key":"e_1_2_7_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2641"},{"key":"e_1_2_7_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3306"},{"key":"e_1_2_7_5_2","doi-asserted-by":"publisher","DOI":"10.1101\/pdb.prot5384"},{"key":"e_1_2_7_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2688"},{"key":"e_1_2_7_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.01.029"},{"key":"e_1_2_7_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"e_1_2_7_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature14248"},{"key":"e_1_2_7_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1193"},{"key":"e_1_2_7_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1094"},{"key":"e_1_2_7_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010017\u20100030\u20107"},{"key":"e_1_2_7_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2012.10.019"},{"key":"e_1_2_7_14_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0904863106"},{"key":"e_1_2_7_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/bfgp\/ely002"},{"key":"e_1_2_7_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt761"},{"key":"e_1_2_7_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1315"},{"key":"e_1_2_7_18_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010016\u20101274\u20104"},{"key":"e_1_2_7_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2013.150"},{"key":"e_1_2_7_20_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz332"},{"key":"e_1_2_7_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4556"},{"key":"e_1_2_7_22_2","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0104s00"},{"key":"e_1_2_7_23_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz348"},{"key":"e_1_2_7_24_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aav1898"},{"key":"e_1_2_7_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3017"},{"key":"e_1_2_7_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_2_7_27_2","first-page":"209","article-title":"Large\u2010scale quality analysis of published ChIP\u2010seq data. 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