{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:10:46Z","timestamp":1760955046198},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.<\/jats:p>\n               <jats:p>Results: We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/gbic.biol.rug.nl\/supplementary<\/jats:p>\n               <jats:p>Contact: \u00a0r.c.jansen@rug.nl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm614","type":"journal-article","created":{"date-parts":[[2007,12,18]],"date-time":"2007-12-18T02:01:49Z","timestamp":1197943309000},"page":"433-434","source":"Crossref","is-referenced-by-count":7,"title":["affyGG: computational protocols for genetical genomics with Affymetrix arrays"],"prefix":"10.1093","volume":"24","author":[{"given":"Rudi","family":"Alberts","sequence":"first","affiliation":[{"name":"Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gonzalo","family":"Vera","sequence":"additional","affiliation":[{"name":"Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ritsert C.","family":"Jansen","sequence":"additional","affiliation":[{"name":"Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,12,16]]},"reference":[{"key":"2023061011435016000_B1","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/S0168-9525(01)02310-1","article-title":"Genetical genomics: the added value from segregation","volume":"17","author":"Jansen","year":"2001","journal-title":"Trends Genet"},{"key":"2023061011435016000_B2","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","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023061011435016000_B3","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1534\/genetics.105.045930","article-title":"A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays","volume":"171","author":"Alberts","year":"2005","journal-title":"Genetics"},{"key":"2023061011435016000_B4","doi-asserted-by":"crossref","first-page":"e262","DOI":"10.1371\/journal.pone.0000622","article-title":"Sequence polymorphisms cause many false cis eQTLs","volume":"2","author":"Alberts","year":"2007","journal-title":"PLoS ONE"},{"key":"2023061011435016000_B5","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/1471-2105-8-132","article-title":"A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat","volume":"8","author":"Alberts","year":"2007","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/3\/433\/50567879\/bioinformatics_24_3_433.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/3\/433\/50567879\/bioinformatics_24_3_433.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T11:44:50Z","timestamp":1686397490000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/3\/433\/254827"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,12,16]]},"references-count":5,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2008,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm614","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,2,1]]},"published":{"date-parts":[[2007,12,16]]}}}