{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T12:46:15Z","timestamp":1774788375241,"version":"3.50.1"},"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2008,1,18]],"date-time":"2008-01-18T00:00:00Z","timestamp":1200614400000},"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.0040005","type":"journal-article","created":{"date-parts":[[2008,1,15]],"date-time":"2008-01-15T15:47:10Z","timestamp":1200412030000},"page":"e5","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":86,"title":["In Silico Detection of Sequence Variations Modifying Transcriptional Regulation"],"prefix":"10.1371","volume":"4","author":[{"given":"Malin C","family":"Andersen","sequence":"first","affiliation":[]},{"given":"P\u00e4r G","family":"Engstr\u00f6m","sequence":"additional","affiliation":[]},{"given":"Stuart","family":"Lithwick","sequence":"additional","affiliation":[]},{"given":"David","family":"Arenillas","sequence":"additional","affiliation":[]},{"given":"Per","family":"Eriksson","sequence":"additional","affiliation":[]},{"given":"Boris","family":"Lenhard","sequence":"additional","affiliation":[]},{"given":"Wyeth W","family":"Wasserman","sequence":"additional","affiliation":[]},{"given":"Jacob","family":"Odeberg","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,1,18]]},"reference":[{"key":"pcbi-0040005-b001","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1248\/bpb.25.1476","article-title":"Structural and functional analysis of a new upstream promoter of the human FAT\/CD36 gene.","volume":"25","year":"2002","journal-title":"Biol Pharm Bull"},{"key":"pcbi-0040005-b002","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1086\/318198","article-title":"A quantitative-trait analysis of human plasma-dopamine beta-hydroxylase activity: evidence for a major functional polymorphism at the DBH locus.","volume":"68","year":"2001","journal-title":"Am J Hum Genet"},{"key":"pcbi-0040005-b003","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1172\/JCI114844","article-title":"An insertion\/deletion polymorphism in the angiotensin I-converting enzyme gene accounting for half the variance of serum enzyme levels.","volume":"86","year":"1990","journal-title":"J Clin Invest"},{"key":"pcbi-0040005-b004","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1056\/NEJM199511023331802","article-title":"The genetic basis of the reduced expression of bilirubin UDP-glucuronosyltransferase 1 in Gilbert's syndrome.","volume":"333","year":"1995","journal-title":"N Engl J Med"},{"key":"pcbi-0040005-b005","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1126\/science.1126431","article-title":"A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter.","volume":"312","year":"2006","journal-title":"Science"},{"key":"pcbi-0040005-b006","first-page":"308","article-title":"Hereditary persistence of alpha-fetoprotein is due to both proximal and distal hepatocyte nuclear factor-1 site mutations.","volume":"126","year":"2004","journal-title":"Gastroenterology"},{"key":"pcbi-0040005-b007","doi-asserted-by":"crossref","first-page":"10739","DOI":"10.1016\/S0021-9258(18)82047-6","article-title":"The two allele sequences of a common polymorphism in the promoter of the plasminogen activator inhibitor-1 (PAI-1) gene respond differently to interleukin-1 in HepG2 cells.","volume":"268","year":"1993","journal-title":"J Biol Chem"},{"key":"pcbi-0040005-b008","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1053\/beha.1999.0038","article-title":"Genetic determinants of arterial thrombosis.","volume":"12","year":"1999","journal-title":"Baillieres Best Pract Res Clin Haematol"},{"key":"pcbi-0040005-b009","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1161\/01.RES.86.9.998","article-title":"Allele-specific regulation of matrix metalloproteinase-12 gene activity is associated with coronary artery luminal dimensions in diabetic patients with manifest coronary artery disease.","volume":"86","year":"2000","journal-title":"Circ Res"},{"key":"pcbi-0040005-b010","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1136\/jmg.2003.014092","article-title":"Functional dimorphism of two hAgRP promoter SNPs in linkage disequilibrium.","volume":"41","year":"2004","journal-title":"J Med Genet"},{"key":"pcbi-0040005-b011","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/sj.ijo.802201","article-title":"The agouti-related protein and body fatness in humans.","volume":"27","year":"2003","journal-title":"Int J Obes Relat Metab Disord"},{"key":"pcbi-0040005-b012","doi-asserted-by":"crossref","first-page":"1991","DOI":"10.1093\/oxfordjournals.molbev.a004023","article-title":"Abundant raw material for cis-regulatory evolution in humans.","volume":"19","year":"2002","journal-title":"Mol Biol Evol"},{"key":"pcbi-0040005-b013","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btk027","article-title":"ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.","volume":"22","year":"2006","journal-title":"Bioinformatics"},{"key":"pcbi-0040005-b014","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1002\/humu.20207","article-title":"Strong bias in the location of functional promoter polymorphisms.","volume":"26","year":"2005","journal-title":"Hum Mutat"},{"key":"pcbi-0040005-b015","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1126\/science.1101659","article-title":"Cis-acting regulatory variation in the human genome.","volume":"306","year":"2004","journal-title":"Science"},{"key":"pcbi-0040005-b016","doi-asserted-by":"crossref","first-page":"12369","DOI":"10.1073\/pnas.210395297","article-title":"Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis.","volume":"97","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040005-b017","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/ng766","article-title":"The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster.","volume":"29","year":"2001","journal-title":"Nat Genet"},{"key":"pcbi-0040005-b018","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1038\/nature02797","article-title":"Genetic analysis of genome-wide variation in human gene expression.","volume":"430","year":"2004","journal-title":"Nature"},{"key":"pcbi-0040005-b019","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/ng992","article-title":"Detection of regulatory variation in mouse genes.","volume":"32","year":"2002","journal-title":"Nat Genet"},{"key":"pcbi-0040005-b020","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/ng1124","article-title":"In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading.","volume":"33","year":"2003","journal-title":"Nat Genet"},{"key":"pcbi-0040005-b021","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1152\/physiolgenomics.00163.2003","article-title":"A survey of genetic and epigenetic variation affecting human gene expression.","volume":"16","year":"2004","journal-title":"Physiol Genomics"},{"key":"pcbi-0040005-b022","article-title":"Local regulatory variation in Saccharomyces cerevisiae.","volume":"1","year":"2005","journal-title":"PLoS Genet"},{"key":"pcbi-0040005-b023","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1186\/1471-2164-7-235","article-title":"Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations.","volume":"7","year":"2006","journal-title":"BMC Genomics"},{"key":"pcbi-0040005-b024","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1093\/bioinformatics\/16.1.16","article-title":"DNA binding sites: representation and discovery.","volume":"16","year":"2000","journal-title":"Bioinformatics"},{"key":"pcbi-0040005-b025","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1006\/jmbi.1996.0760","article-title":"Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome.","volume":"266","year":"1997","journal-title":"J Mol Biol"},{"key":"pcbi-0040005-b026","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1128\/MCB.16.1.437","article-title":"Quantitative discrimination of MEF2 sites.","volume":"16","year":"1996","journal-title":"Mol Cell Biol"},{"key":"pcbi-0040005-b027","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/79965","article-title":"Human-mouse genome comparisons to locate regulatory sites.","volume":"26","year":"2000","journal-title":"Nat Genet"},{"key":"pcbi-0040005-b028","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1475-4924-2-13","article-title":"Identification of conserved regulatory elements by comparative genome analysis.","volume":"2","year":"2003","journal-title":"J Biol"},{"key":"pcbi-0040005-b029","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/nrg1315","article-title":"Applied bioinformatics for the identification of regulatory elements.","volume":"5","year":"2004","journal-title":"Nat Rev Genet"},{"key":"pcbi-0040005-b030","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1006\/jmbi.1997.1171","article-title":"Quantitative specificity of the Mnt repressor.","volume":"271","year":"1997","journal-title":"J Mol Biol"},{"issue":"Database issue","key":"pcbi-0040005-b031","first-page":"D91","article-title":"JASPAR: an open-access database for eukaryotic transcription factor binding profiles.","volume":"32","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040005-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-0040005-b033","doi-asserted-by":"crossref","first-page":"2151","DOI":"10.1101\/gr.199801","article-title":"GeneLynx: a gene-centric portal to the human genome.","volume":"11","year":"2001","journal-title":"Genome Res"},{"key":"pcbi-0040005-b034","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","year":"2001","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"pcbi-0040005-b035","first-page":"D516","article-title":"HGVbase: a curated resource describing human DNA variation and phenotype relationships.","volume":"32","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040005-b036","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1038\/ng0403-439","article-title":"Wanted: regulatory SNPs.","volume":"33","year":"2003","journal-title":"Nat Genet"},{"key":"pcbi-0040005-b037","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1126\/science.1131007","article-title":"A systems approach to measuring the binding energy landscapes of transcription factors.","volume":"315","year":"2007","journal-title":"Science"},{"key":"pcbi-0040005-b038","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","year":"2000","journal-title":"Nat Genet"},{"key":"pcbi-0040005-b039","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1074\/mcp.M500279-MCP200","article-title":"A human protein atlas for normal and cancer tissues based on antibody proteomics.","volume":"4","year":"2005","journal-title":"Mol Cell Proteomics"},{"key":"pcbi-0040005-b040","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1093\/hmg\/ddm066","article-title":"Identification of polymorphic antioxidant response elements in the human genome.","volume":"16","year":"2007","journal-title":"Hum Mol Genet"},{"key":"pcbi-0040005-b041","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/j.mcp.2006.03.007","article-title":"Potential regulatory SNPs in promoters of human genes: a systematic approach.","volume":"20","year":"2006","journal-title":"Mol Cell Probes"},{"key":"pcbi-0040005-b042","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles.","volume":"31","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040005-b043","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1002\/humu.20049","article-title":"PromoLign: a database for upstream region analysis and SNPs.","volume":"23","year":"2004","journal-title":"Hum Mutat"},{"key":"pcbi-0040005-b044","article-title":"A survey of genomic properties for the detection of regulatory polymorphisms.","volume":"3","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"pcbi-0040005-b045","doi-asserted-by":"crossref","first-page":"3154","DOI":"10.1093\/nar\/gki624","article-title":"oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes.","volume":"33","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040005-b046","doi-asserted-by":"crossref","first-page":"8317","DOI":"10.1016\/S0021-9258(18)53098-2","article-title":"Analysis of heat shock element recognition by saturation mutagenesis of the human HSP70.1 gene promoter.","volume":"268","year":"1993","journal-title":"J Biol Chem"},{"key":"pcbi-0040005-b047","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-0040005-b048","unstructured":"Team RDC 2005 R: A language and environment for statistical computing Computing RFfS, editor. Vienna, Austria"},{"key":"pcbi-0040005-b049","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1101\/gr.361602","article-title":"The Bioperl toolkit: Perl modules for the life sciences.","volume":"12","year":"2002","journal-title":"Genome Res"},{"key":"pcbi-0040005-b050","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1093\/nar\/gkg129","article-title":"The UCSC Genome Browser Database.","volume":"31","year":"2003","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040005","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T20:19:32Z","timestamp":1630527572000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040005"}},"subtitle":[],"editor":[{"given":"Gary","family":"Stormo","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,1,18]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2008,1,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0040005","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,18]]}}}