| 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 |
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|
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
Otani, Keiko
Hiyama, Keiko
Kamei, Naomi
Satoh, Kenichi
Hiyama, Eiso
|
| アクセス権 |
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|
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 |
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|
権利情報 |
Copyright (c) 2010 Ohtaki et al; licensee BioMed Central Ltd. |
| 主題 |
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主題Scheme |
NDC |
|
主題 |
490 |
| 内容記述 |
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|
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 |
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|
出版者 |
BioMed Central Ltd |
| 言語 |
|
|
言語 |
eng |
| 資源タイプ |
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|
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 |
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|
識別子タイプ |
DOI |
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|
関連識別子 |
10.1186/1471-2105-11-183 |
| 関連情報 |
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|
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 |
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収録物識別子タイプ |
ISSN |
|
収録物識別子 |
1471-2105 |
| 収録物識別子 |
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|
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 |
BMC-Bioinformatics_11_183.pdf (819.7 KB)
