{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T10:41:53Z","timestamp":1776249713512,"version":"3.50.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present a tool designed to characterize genome-wide protein\u2013DNA interaction patterns from ChIP-chip and ChIP-Seq data. This stand-alone extension of our web application CEAS (cis-regulatory element annotation system) provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic regions, particularly allowing observation of continuous and broad ChIP enrichment that might be too subtle to detect from ChIP peaks alone.<\/jats:p>\n               <jats:p>Availability: The CEAS Python package is publicly available at http:\/\/liulab.dfci.harvard.edu\/CEAS.<\/jats:p>\n               <jats:p>Contact: \u00a0shin@jimmy.harvard.edu; xsliu@jimmy.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp479","type":"journal-article","created":{"date-parts":[[2009,8,19]],"date-time":"2009-08-19T03:03:10Z","timestamp":1250650990000},"page":"2605-2606","source":"Crossref","is-referenced-by-count":403,"title":["CEAS: <i>cis<\/i>-regulatory element annotation system"],"prefix":"10.1093","volume":"25","author":[{"given":"Hyunjin","family":"Shin","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115 and 2Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA"}]},{"given":"Tao","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115 and 2Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA"}]},{"given":"Arjun K.","family":"Manrai","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115 and 2Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA"}]},{"given":"X. Shirley","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115 and 2Harvard-MIT Division of Health Sciences and Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,8,18]]},"reference":[{"key":"2023013112125017000_B1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2023013112125017000_B2","doi-asserted-by":"crossref","first-page":"W551","DOI":"10.1093\/nar\/gkl322","article-title":"CEAS: cis-regulatory element annotation system","volume":"34","author":"Ji","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023013112125017000_B3","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/nbt.1505","article-title":"An integrated software system for analyzing ChIP-chip and ChIP-seq data","volume":"26","author":"Ji","year":"2008","journal-title":"Nat. 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