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A robust method for estimating gene expression states using Affymetrix microarray probe level data

https://hiroshima.repo.nii.ac.jp/records/2006502
https://hiroshima.repo.nii.ac.jp/records/2006502
441e1cb9-eb2f-4e89-8c9f-15a4f1aad2a2
名前 / ファイル ライセンス アクション
BMC-Bioinformatics_11_183.pdf BMC-Bioinformatics_11_183.pdf (819.7 KB)
Item type デフォルトアイテムタイプ_(フル)(1)
公開日 2023-03-18
タイトル
タイトル A robust method for estimating gene expression states using Affymetrix microarray probe level data
言語 en
作成者 Ohtaki, Megu

× Ohtaki, Megu

en Ohtaki, Megu

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Otani, Keiko

× Otani, Keiko

en Otani, Keiko

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Hiyama, Keiko

× Hiyama, Keiko

en Hiyama, Keiko

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Kamei, Naomi

× Kamei, Naomi

en Kamei, Naomi

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Satoh, Kenichi

× Satoh, Kenichi

en Satoh, Kenichi

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Hiyama, Eiso

× Hiyama, Eiso

en Hiyama, Eiso

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アクセス権
アクセス権 open access
アクセス権URI http://purl.org/coar/access_right/c_abf2
権利情報
権利情報 Copyright (c) 2010 Ohtaki et al; licensee BioMed Central Ltd.
主題
主題Scheme NDC
主題 490
内容記述
内容記述 Background: Microarray technology is a high-throughput method for measuring the expression levels of thousand of genes simultaneously. The observed intensities combine a non-specific binding, which is a major disadvantage with microarray data. The Affymetrix GeneChip assigned a mismatch (MM) probe with the intention of measuring nonspecific binding, but various opinions exist regarding usefulness of MM measures. It should be noted that not all observed intensities are associated with expressed genes and many of those are associated with unexpressed genes, of which measured values express mere noise due to non-specific binding, cross-hybridization, or stray signals. The implicit assumption that all genes are expressed leads to poor performance of microarray data analyses. We assume two functional states of a gene - expressed or unexpressed - and propose a robust method to estimate gene expression states using an order relationship between PM and MM measures. Results: An indicator 'probability of a gene being expressed' was obtained using the number of probe pairs within a probe set where the PM measure exceeds the MM measure. We examined the validity of the proposed indicator using Human Genome U95 data sets provided by Affymetrix. The usefulness of 'probability of a gene being expressed' is illustrated through an exploration of candidate genes involved in neuroblastoma prognosis. We identified the candidate genes for which expression states differed (un-expressed or expressed) when compared between two outcomes. The validity of this result was subsequently confirmed by quantitative RT-PCR. Conclusion: The proposed qualitative evaluation, 'probability of a gene being expressed', is a useful indicator for improving microarray data analysis. It is useful to reduce the number of false discoveries. Expression states - expressed or unexpressed - correspond to the most fundamental gene function 'On' and 'Off', which can lead to biologically meaningful results.
言語 en
出版者
出版者 BioMed Central Ltd
言語
言語 eng
資源タイプ
資源タイプ識別子 http://purl.org/coar/resource_type/c_6501
資源タイプ journal article
出版タイプ
出版タイプ VoR
出版タイプResource http://purl.org/coar/version/c_970fb48d4fbd8a85
関連情報
識別子タイプ DOI
関連識別子 10.1186/1471-2105-11-183
関連情報
識別子タイプ DOI
関連識別子 http://dx.doi.org/10.1186/1471-2105-11-183
収録物識別子
収録物識別子タイプ ISSN
収録物識別子 1471-2105
収録物識別子
収録物識別子タイプ NCID
収録物識別子 AA12034719
開始ページ
開始ページ 183-1
書誌情報 BMC Bioinformatics
BMC Bioinformatics

巻 11, 号 183, p. 183-1-183-14, 発行日 2010-04-12
旧ID 30398
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