{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T02:42:02Z","timestamp":1770777722850,"version":"3.50.0"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,12,1]],"date-time":"2010-12-01T00:00:00Z","timestamp":1291161600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2010,12,17]],"date-time":"2010-12-17T00:00:00Z","timestamp":1292544000000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 million single nucleotide polymorphisms (SNPs) in the same individuals are publicly available. We aimed to generate a user-friendly web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest, which is also well-known as an expression quantitative trait locus (eQTL) analysis.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>SNPexp is implemented as a server-side script, and publicly available on this website: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/tinyurl.com\/snpexp\" ext-link-type=\"uri\">http:\/\/tinyurl.com\/snpexp<\/jats:ext-link>. Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>SNPexp provides a convenient and platform-independent way to calculate and visualize the correlation between HapMap genotypes within a specified genetic region anywhere in the genome and gene expression levels. This allows for investigation of both cis and trans effects. The web interface and utilization of publicly available and widely used software resources makes it an attractive supplement to more advanced bioinformatic tools. For the advanced user the program can be used on a local computer on custom datasets.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-600","type":"journal-article","created":{"date-parts":[[2011,1,5]],"date-time":"2011-01-05T19:27:00Z","timestamp":1294255620000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":79,"title":["SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels"],"prefix":"10.1186","volume":"11","author":[{"given":"Kristian","family":"Holm","sequence":"first","affiliation":[]},{"given":"Espen","family":"Melum","sequence":"additional","affiliation":[]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[]},{"given":"Tom H","family":"Karlsen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,12,17]]},"reference":[{"key":"4183_CR1","unstructured":"NCBI dbSNP build 131[http:\/\/www.ncbi.nlm.nih.gov\/projects\/SNP]"},{"key":"4183_CR2","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1093\/nar\/29.1.308","volume":"29","author":"ST Sherry","year":"2001","unstructured":"Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001, 29: 308\u2013311. 10.1093\/nar\/29.1.308","journal-title":"Nucleic Acids Res"},{"key":"4183_CR3","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.ajhg.2008.06.008","volume":"83","author":"CA Anderson","year":"2008","unstructured":"Anderson CA, Pettersson FH, Barrett JC, Zhuang JJ, Ragoussis J, Cardon LR, Morris AP: Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms. Am J Hum Genet 2008, 83: 112\u2013119. 10.1016\/j.ajhg.2008.06.008","journal-title":"Am J Hum Genet"},{"key":"4183_CR4","unstructured":"Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA: A Catalog of Published Genome-Wide Association Studies.[http:\/\/www.genome.gov\/gwastudies] Accessed 16.06.2010"},{"key":"4183_CR5","doi-asserted-by":"publisher","first-page":"9362","DOI":"10.1073\/pnas.0903103106","volume":"106","author":"LA Hindorff","year":"2009","unstructured":"Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106: 9362\u20139367. 10.1073\/pnas.0903103106","journal-title":"Proc Natl Acad Sci USA"},{"key":"4183_CR6","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1038\/nrg2630","volume":"10","author":"VG Cheung","year":"2009","unstructured":"Cheung VG, Spielman RS: Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat Rev Genet 2009, 10: 595\u2013604. 10.1038\/nrg2630","journal-title":"Nat Rev Genet"},{"key":"4183_CR7","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1038\/ng2109","volume":"39","author":"AL Dixon","year":"2007","unstructured":"Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, Wong KC, Taylor J, Burnett E, Gut I, Farrall M, Lathrop GM, Abecasis GR, Cookson WO: A genome-wide association study of global gene expression. Nat Genet 2007, 39: 1202\u20131207. 10.1038\/ng2109","journal-title":"Nat Genet"},{"key":"4183_CR8","doi-asserted-by":"publisher","first-page":"e107","DOI":"10.1371\/journal.pbio.0060107","volume":"6","author":"EE Schadt","year":"2008","unstructured":"Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, vila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, et al.: Mapping the genetic architecture of gene expression in human liver. PLoS Biol 2008, 6: e107. 10.1371\/journal.pbio.0060107","journal-title":"PLoS Biol"},{"key":"4183_CR9","doi-asserted-by":"publisher","first-page":"e1000214","DOI":"10.1371\/journal.pgen.1000214","volume":"4","author":"JB Veyrieras","year":"2008","unstructured":"Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK: High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 2008, 4: e1000214. 10.1371\/journal.pgen.1000214","journal-title":"PLoS Genet"},{"key":"4183_CR10","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1038\/nrg2537","volume":"10","author":"W Cookson","year":"2009","unstructured":"Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M: Mapping complex disease traits with global gene expression. Nat Rev Genet 2009, 10: 184\u2013194. 10.1038\/nrg2537","journal-title":"Nat Rev Genet"},{"key":"4183_CR11","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1093\/bioinformatics\/btn648","volume":"25","author":"DM Gatti","year":"2009","unstructured":"Gatti DM, Shabalin AA, Lam TC, Wright FA, Rusyn I, Nobel AB: FastMap: fast eQTL mapping in homozygous populations. Bioinformatics 2009, 25: 482\u2013489. 10.1093\/bioinformatics\/btn648","journal-title":"Bioinformatics"},{"key":"4183_CR12","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-8-7","volume":"8","author":"W Zou","year":"2007","unstructured":"Zou W, Aylor DL, Zeng ZB: eQTL Viewer: visualizing how sequence variation affects genome-wide transcription. BMC Bioinformatics 2007, 8: 7. 10.1186\/1471-2105-8-7","journal-title":"BMC Bioinformatics"},{"key":"4183_CR13","unstructured":"eQTL Browser at the Pritchard lab[http:\/\/eqtl.uchicago.edu\/cgi-bin\/gbrowse\/eqtl]"},{"key":"4183_CR14","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/nature06258","volume":"449","author":"KA Frazer","year":"2007","unstructured":"Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, et al.: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449: 851\u2013861. 10.1038\/nature06258","journal-title":"Nature"},{"key":"4183_CR15","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1126\/science.1136678","volume":"315","author":"BE Stranger","year":"2007","unstructured":"Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315: 848\u2013853. 10.1126\/science.1136678","journal-title":"Science"},{"key":"4183_CR16","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/nature02168","volume":"426","author":"The International HapMap Consortium","year":"2003","unstructured":"The International HapMap Consortium: The International HapMap Project. Nature 2003, 426: 789\u2013796. 10.1038\/nature02168","journal-title":"Nature"},{"key":"4183_CR17","unstructured":"Larry Wall: The Perl Programming Language, version 5.10[http:\/\/www.perl.org]"},{"key":"4183_CR18","unstructured":"The Apache Software Foundation[http:\/\/www.apache.org]"},{"key":"4183_CR19","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81: 559\u2013575. 10.1086\/519795","journal-title":"Am J Hum Genet"},{"key":"4183_CR20","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1101\/gr.229102. Article published online before print in May 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res 2002, 12: 996\u20131006.","journal-title":"Genome Res"},{"key":"4183_CR21","unstructured":"PLINK v1.06 by Shaun Purcell[http:\/\/pngu.mgh.harvard.edu\/purcell\/plink]"},{"key":"4183_CR22","unstructured":"HapMap phase III release 3 (consensus)[http:\/\/www.sanger.ac.uk\/humgen\/hapmap3]"},{"key":"4183_CR23","unstructured":"Genevar - GENe Expression VARiation[http:\/\/www.sanger.ac.uk\/humgen\/genevar]"},{"key":"4183_CR24","unstructured":"UCSC Genome Browser[http:\/\/genome.ucsc.edu\/cgi-bin\/hgGateway]"},{"key":"4183_CR25","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/nature06014","volume":"448","author":"MF Moffatt","year":"2007","unstructured":"Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, Heath S, Depner M, von Berg A, Bufe A, Rietschel E, Heinzmann A, Simma B, Frischer T, Willis-Owen SA, Wong KC, Illig T, Vogelberg C, Weiland SK, von Mutius E, Abecasis GR, Farrall M, Gut IG, Lathrop GM, Cookson WO: Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 2007, 448: 470\u2013473. 10.1038\/nature06014","journal-title":"Nature"},{"key":"4183_CR26","unstructured":"Bioportal at University of Oslo[http:\/\/www.bioportal.uio.no\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-600.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-600\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-600.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T12:14:14Z","timestamp":1630498454000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-600"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,12]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["4183"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-600","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,12]]},"assertion":[{"value":"7 July 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 December 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 December 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"600"}}