{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T22:10:16Z","timestamp":1675203016421},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2715,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Whole-genome microarrays allow us to interrogate the entire transcriptome of a cell. Affymetrix microarrays are constructed using several probes that match to different regions of a gene and a summarization step reduces this complexity into a single value, representing the expression level of the gene or the expression level of an exon in the case of exon arrays. However, this simplification eliminates information that might be useful when focusing on specific genes of interest. To address these limitations, we present a software package for the R platform that allows detailed analysis of expression at the probe level. The package matches the probe sequences against a target gene sequence (either mRNA or DNA) and shows the expression levels of each probe along the gene. It also features functions to fit a linear regression based on several genetic models that enables study of the relationship between gene expression and genotype.<\/jats:p>\n               <jats:p>Availability and implementation: The software is implemented as a platform-independent R package available through the Bioconductor repository at http:\/\/www.bioconductor.org\/. It is licensed as GPL 2.0.<\/jats:p>\n               <jats:p>Contact: \u00a0lasse.folkersen@ki.se<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp279","type":"journal-article","created":{"date-parts":[[2009,4,28]],"date-time":"2009-04-28T00:25:20Z","timestamp":1240878320000},"page":"1978-1979","source":"Crossref","is-referenced-by-count":5,"title":["GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome"],"prefix":"10.1093","volume":"25","author":[{"given":"Lasse","family":"Folkersen","sequence":"first","affiliation":[{"name":"1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Diego","family":"Diez","sequence":"additional","affiliation":[{"name":"1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Craig E.","family":"Wheelock","sequence":"additional","affiliation":[{"name":"1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Jesper Z.","family":"Haeggstr\u00f6m","sequence":"additional","affiliation":[{"name":"1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Susumu","family":"Goto","sequence":"additional","affiliation":[{"name":"1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Per","family":"Eriksson","sequence":"additional","affiliation":[{"name":"1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden"}]},{"given":"Anders","family":"Gabrielsen","sequence":"additional","affiliation":[{"name":"1 Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden, 2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 Japan and 3 Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2009,4,27]]},"reference":[{"key":"2023013112100682200_B1","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1161\/STROKEAHA.107.491969","article-title":"Genetic variation in members of the leukotriene biosynthesis pathway confer an increased risk of ischemic stroke: a replication study in two independent populations","volume":"39","author":"Bevan","year":"2008","journal-title":"Stroke"},{"key":"2023013112100682200_B2","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013112100682200_B3","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023013112100682200_B4","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nature02168","article-title":"The International HapMap Project","volume":"426","author":"HapMap","year":"2003","journal-title":"Nature"},{"key":"2023013112100682200_B5","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/ng.2007.57","article-title":"Genome-wide analysis of transcript isoform variation in humans","volume":"40","author":"Kwan","year":"2008","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1978\/48994654\/bioinformatics_25_15_1978.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1978\/48994654\/bioinformatics_25_15_1978.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:31:38Z","timestamp":1675200698000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/15\/1978\/210902"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,4,27]]},"references-count":5,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2009,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp279","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,8,1]]},"published":{"date-parts":[[2009,4,27]]}}}