{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T10:29:29Z","timestamp":1760783369464},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2048,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>We have implemented aggregation and correlation toolbox (ACT), an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project. It is able to generate aggregate profiles of a given track around a set of specified anchor points, such as transcription start sites. It is also able to correlate related tracks and analyze them for saturation\u2013i.e. how much of a certain feature is covered with each new succeeding experiment. The ACT site contains downloadable code in a variety of formats, interactive web servers (for use on small quantities of data), example datasets, documentation and a gallery of outputs. Here, we explain the components of the toolbox in more detail and apply them in various contexts.<\/jats:p>\n               <jats:p>Availability: ACT is available at http:\/\/act.gersteinlab.org<\/jats:p>\n               <jats:p>Contact: \u00a0pi@gersteinlab.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr092","type":"journal-article","created":{"date-parts":[[2011,2,25]],"date-time":"2011-02-25T01:38:20Z","timestamp":1298597900000},"page":"1152-1154","source":"Crossref","is-referenced-by-count":32,"title":["ACT: aggregation and correlation toolbox for analyses of genome tracks"],"prefix":"10.1093","volume":"27","author":[{"given":"Justin","family":"Jee","sequence":"first","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Joel","family":"Rozowsky","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Kevin Y.","family":"Yip","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Lucas","family":"Lochovsky","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Robert","family":"Bjornson","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Guoneng","family":"Zhong","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Zhengdong","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Yutao","family":"Fu","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Jie","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Zhiping","family":"Weng","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular, Cellular and Developmental Biology, 3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA, 4Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, 5Department of Computer Science, Yale University, New Haven, CT, 6Bioinformatics Program, Boston University, Boston and 7Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,2,23]]},"reference":[{"key":"2023061311474203200_B1","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1101\/gr.092197.109","article-title":"The first Korean genome sequence and 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Biol."},{"key":"2023061311474203200_B10","first-page":"927","article-title":"Unlocking the secrets of the genome","volume":"18","author":"modENCODE Consortium","year":"2009","journal-title":"Nature"},{"key":"2023061311474203200_B11","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sharry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023061311474203200_B12","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1101\/gr.5573107","article-title":"Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions","volume":"17","author":"Zhang","year":"2007","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/8\/1152\/50580334\/bioinformatics_27_8_1152.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/8\/1152\/50580334\/bioinformatics_27_8_1152.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T11:49:40Z","timestamp":1686656980000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/8\/1152\/228311"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,23]]},"references-count":12,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2011,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr092","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,4,15]]},"published":{"date-parts":[[2011,2,23]]}}}