{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T19:00:44Z","timestamp":1776020444995,"version":"3.50.1"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2007,4,6]],"date-time":"2007-04-06T00:00:00Z","timestamp":1175817600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.0030063","type":"journal-article","created":{"date-parts":[[2007,4,4]],"date-time":"2007-04-04T16:15:58Z","timestamp":1175703358000},"page":"e63","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function"],"prefix":"10.1371","volume":"3","author":[{"given":"Yili","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas W","family":"Blackwell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ji","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angel W","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David J","family":"States","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2007,4,6]]},"reference":[{"key":"pcbi-0030063-b001","first-page":"M135","article-title":"Function of the c-Myc oncoprotein in chromatin remodeling and transcription.","volume":"1471","year":"2001","journal-title":"Biochim Biophys Acta"},{"key":"pcbi-0030063-b002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/MCB.19.1.1","article-title":"c-Myc target genes involved in cell growth, apoptosis, and metabolism.","volume":"19","year":"1999","journal-title":"Mol Cell Biol"},{"key":"pcbi-0030063-b003","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1006\/excr.1999.4686","article-title":"Function of the c-Myc oncogenic transcription factor.","volume":"253","year":"1999","journal-title":"Exp Cell Res"},{"key":"pcbi-0030063-b004","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/sj.onc.1201939","article-title":"Involvement of Myc targets in c-Myc and N-Myc induced human tumors.","volume":"17","year":"1998","journal-title":"Oncogene"},{"key":"pcbi-0030063-b005","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1096\/fasebj.12.9.633","article-title":"The molecular role of Myc in growth and transformation: Recent discoveries lead to new insights.","volume":"12","year":"1998","journal-title":"Faseb J"},{"key":"pcbi-0030063-b006","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0014-4827(02)00020-4","article-title":"Mechanisms of c-myc\u2013mediated transcriptional repression of growth arrest genes.","volume":"283","year":"2003","journal-title":"Exp Cell Res"},{"key":"pcbi-0030063-b007","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1016\/S0960-9822(03)00297-5","article-title":"Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression.","volume":"13","year":"2003","journal-title":"Curr Biol"},{"key":"pcbi-0030063-b008","doi-asserted-by":"crossref","first-page":"10470","DOI":"10.1016\/S0021-9258(19)50042-4","article-title":"DNA binding activities of c-Myc purified from eukaryotic cells.","volume":"267","year":"1992","journal-title":"J Biol Chem"},{"key":"pcbi-0030063-b009","doi-asserted-by":"crossref","first-page":"3205","DOI":"10.1093\/nar\/27.15.3205","article-title":"Specificity of DNA binding of the c-Myc\/Max and ARNT\/ARNT dimers at the CACGTG recognition site.","volume":"27","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0030063-b010","first-page":"5922","article-title":"Identification of c-Myc responsive genes using rat cDNA microarray.","volume":"60","year":"2000","journal-title":"Cancer Res"},{"key":"pcbi-0030063-b011","doi-asserted-by":"crossref","first-page":"36921","DOI":"10.1074\/jbc.M201493200","article-title":"Identifying genes regulated in a Myc-dependent manner.","volume":"277","year":"2002","journal-title":"J Biol Chem"},{"key":"pcbi-0030063-b012","doi-asserted-by":"crossref","first-page":"12563","DOI":"10.1074\/jbc.M210462200","article-title":"A large scale genetic analysis of c-Myc-regulated gene expression patterns.","volume":"278","year":"2003","journal-title":"J Biol Chem"},{"key":"pcbi-0030063-b013","doi-asserted-by":"crossref","first-page":"8164","DOI":"10.1073\/pnas.1332764100","article-title":"A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells.","volume":"100","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b014","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/ng1532","article-title":"Reverse engineering of regulatory networks in human B cells.","volume":"37","year":"2005","journal-title":"Nat Genet"},{"key":"pcbi-0030063-b015","doi-asserted-by":"crossref","first-page":"6902","DOI":"10.1073\/pnas.0502081102","article-title":"Targeting c-Myc-activated genes with a correlation method: Detection of global changes in large gene expression network dynamics.","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b016","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S0378-1119(02)00668-6","article-title":"A computerized database-scan to identify c-MYC targets.","volume":"292","year":"2002","journal-title":"Gene"},{"key":"pcbi-0030063-b017","doi-asserted-by":"crossref","first-page":"R69","DOI":"10.1186\/gb-2003-4-10-r69","article-title":"An integrated database of genes responsive to the Myc oncogenic transcription factor: Identification of direct genomic targets.","volume":"4","year":"2003","journal-title":"Genome Biol"},{"key":"pcbi-0030063-b018","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.1073\/pnas.0931346100","article-title":"A strategy for identifying transcription factor binding sites reveals two classes of genomic c-Myc target sites.","volume":"100","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b019","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1101\/gad.1067003","article-title":"Genomic targets of the human c-Myc protein.","volume":"17","year":"2003","journal-title":"Genes Dev"},{"key":"pcbi-0030063-b020","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/ng0595-20","article-title":"CpNpG methylation in mammalian cells.","volume":"10","year":"1995","journal-title":"Nat Genet"},{"key":"pcbi-0030063-b021","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/0092-8674(85)90312-5","article-title":"A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA.","volume":"40","year":"1985","journal-title":"Cell"},{"key":"pcbi-0030063-b022","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1126\/science.1987636","article-title":"Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region.","volume":"251","year":"1991","journal-title":"Science"},{"key":"pcbi-0030063-b023","doi-asserted-by":"crossref","first-page":"12117","DOI":"10.1073\/pnas.0409097102","article-title":"In vivo transcriptional regulation of N-Myc target genes is controlled by E-box methylation.","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b024","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S0092-8674(04)00044-3","article-title":"The nucleosome: From genomic organization to genomic regulation.","volume":"116","year":"2004","journal-title":"Cell"},{"key":"pcbi-0030063-b025","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1038\/ncb1434","article-title":"Myc-binding\u2013site recognition in the human genome is determined by chromatin context.","volume":"8","year":"2006","journal-title":"Nat Cell Biol"},{"key":"pcbi-0030063-b026","doi-asserted-by":"crossref","first-page":"4459","DOI":"10.1073\/pnas.0501076102","article-title":"Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues.","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b027","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1038\/ng1909","article-title":"DNA methylation profiling of human chromosomes 6, 20, and 22.","volume":"38","year":"2006","journal-title":"Nat Genet"},{"key":"pcbi-0030063-b028","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1093\/nar\/24.1.238","article-title":"TRANSFAC: A database on transcription factors and their DNA binding sites.","volume":"24","year":"1996","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0030063-b029","doi-asserted-by":"crossref","first-page":"5372","DOI":"10.1093\/nar\/21.23.5372","article-title":"Distinct DNA binding preferences for the c-Myc\/Max and Max\/Max dimers.","volume":"21","year":"1993","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0030063-b030","doi-asserted-by":"crossref","first-page":"D91","DOI":"10.1093\/nar\/gkh012","article-title":"JASPAR: An open-access database for eukaryotic transcription factor binding profiles.","volume":"32","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0030063-b031","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1093\/bioinformatics\/18.8.1135","article-title":"TFBS: Computational framework for transcription factor binding site analysis.","volume":"18","year":"2002","journal-title":"Bioinformatics"},{"key":"pcbi-0030063-b032","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.","volume":"15","year":"2005","journal-title":"Genome Res"},{"key":"pcbi-0030063-b033","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1101\/gad.1272505","article-title":"Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping.","volume":"19","year":"2005","journal-title":"Genes Dev"},{"key":"pcbi-0030063-b034","unstructured":"IanHWittenEF 2005 Data mining: Practical machine learning tools and techniques San Francisco Morgan Kaufmann 525"},{"key":"pcbi-0030063-b035","doi-asserted-by":"crossref","first-page":"17834","DOI":"10.1073\/pnas.0604129103","article-title":"Global mapping of c-Myc binding sites and target gene networks in human B cells.","volume":"103","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b036","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/S0092-8674(04)00127-8","article-title":"Unbiased mapping of transcription factor binding sites along human Chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.","volume":"116","year":"2004","journal-title":"Cell"},{"key":"pcbi-0030063-b037","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/S1535-6108(02)00030-2","article-title":"Gene expression correlates of clinical prostate cancer behavior.","volume":"1","year":"2002","journal-title":"Cancer Cell"},{"key":"pcbi-0030063-b038","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: Open software development for computational biology and bioinformatics.","volume":"5","year":"2004","journal-title":"Genome Biol"},{"key":"pcbi-0030063-b039","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data.","volume":"4","year":"2003","journal-title":"Biostatistics"},{"key":"pcbi-0030063-b040","doi-asserted-by":"crossref","first-page":"2590","DOI":"10.1038\/sj.emboj.7600742","article-title":"Stress response gene ATF3 is a target of c-Myc in serum-induced cell proliferation.","volume":"24","year":"2005","journal-title":"EMBO J"},{"key":"pcbi-0030063-b041","doi-asserted-by":"crossref","first-page":"14649","DOI":"10.1074\/jbc.M308842200","article-title":"Direct activation of HSP90A transcription by c-Myc contributes to c-Myc\u2013induced transformation.","volume":"279","year":"2004","journal-title":"J Biol Chem"},{"key":"pcbi-0030063-b042","doi-asserted-by":"crossref","first-page":"7143","DOI":"10.1073\/pnas.93.14.7143","article-title":"ECA39, a conserved gene regulated by c-Myc in mice, is involved in G1\/S cell cycle regulation in yeast.","volume":"93","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b043","doi-asserted-by":"crossref","first-page":"4032","DOI":"10.1128\/MCB.14.6.4032","article-title":"Repression of cyclin D1: A novel function of MYC.","volume":"14","year":"1994","journal-title":"Mol Cell Biol"},{"key":"pcbi-0030063-b044","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1126\/science.256.5055.379","article-title":"Reciprocal regulation of adipogenesis by Myc and C\/EBP alpha.","volume":"256","year":"1992","journal-title":"Science"},{"key":"pcbi-0030063-b045","doi-asserted-by":"crossref","first-page":"3093","DOI":"10.1128\/MCB.13.5.3093","article-title":"Overexpression of Myc suppresses CCAAT transcription factor\/nuclear factor 1\u2013dependent promoters in vivo.","volume":"13","year":"1993","journal-title":"Mol Cell Biol"},{"key":"pcbi-0030063-b046","doi-asserted-by":"crossref","first-page":"6768","DOI":"10.1128\/MCB.20.18.6768-6778.2000","article-title":"Myc is an essential negative regulator of platelet-derived growth factor beta receptor expression.","volume":"20","year":"2000","journal-title":"Mol Cell Biol"},{"key":"pcbi-0030063-b047","doi-asserted-by":"crossref","first-page":"24270","DOI":"10.1074\/jbc.274.34.24270","article-title":"Cell cycle\u2013dependent switch of up- and down-regulation of human hsp70 gene expression by interaction between c-Myc and CBF\/NF-Y.","volume":"274","year":"1999","journal-title":"J Biol Chem"},{"key":"pcbi-0030063-b048","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.semcancer.2006.07.014","article-title":"The c-Myc target gene network.","volume":"16","year":"2006","journal-title":"Semin Cancer Biol"},{"key":"pcbi-0030063-b049","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/0022-2836(87)90689-9","article-title":"CpG islands in vertebrate genomes.","volume":"196","year":"1987","journal-title":"J Mol Biol"},{"key":"pcbi-0030063-b050","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/ng0394-236","article-title":"Purification of CpG islands using a methylated DNA binding column.","volume":"6","year":"1994","journal-title":"Nat Genet"},{"key":"pcbi-0030063-b051","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1007\/s003350010071","article-title":"CpG island libraries from human Chromosomes 18 and 22: Landmarks for novel genes.","volume":"11","year":"2000","journal-title":"Mamm Genome"},{"key":"pcbi-0030063-b052","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing.","volume":"57","year":"1995","journal-title":"J Roy Statist Soc Ser B"},{"key":"pcbi-0030063-b053","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1073\/pnas.2536479100","article-title":"In silico dissection of cell-type\u2013associated patterns of gene expression in prostate cancer.","volume":"101","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b054","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1200\/JCO.2004.05.158","article-title":"Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy.","volume":"22","year":"2004","journal-title":"J Clin Oncol"},{"key":"pcbi-0030063-b055","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1016\/S0140-6736(03)13308-9","article-title":"Gene expression predictors of breast cancer outcomes.","volume":"361","year":"2003","journal-title":"Lancet"},{"key":"pcbi-0030063-b056","doi-asserted-by":"crossref","first-page":"13790","DOI":"10.1073\/pnas.191502998","article-title":"Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.","volume":"98","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030063-b057","first-page":"459","article-title":"In chronic myeloid leukemia white cells from cytogenetic responders and non-responders to imatinib have very similar gene expression signatures.","volume":"90","year":"2005","journal-title":"Haematologica"},{"key":"pcbi-0030063-b058","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/ng1151","article-title":"Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells.","volume":"34","year":"2003","journal-title":"Nat Genet"},{"key":"pcbi-0030063-b059","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/ng765","article-title":"MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia.","volume":"30","year":"2002","journal-title":"Nat Genet"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030063","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,15]],"date-time":"2025-01-15T13:55:13Z","timestamp":1736949313000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030063"}},"subtitle":[],"editor":[{"given":"Philip E","family":"Bourne","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2007,4,6]]},"references-count":59,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2007,4,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0030063","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,4,6]]}}}