Detail DNA microarray normalization methods can remove bias from differential protein expression analysis of 2-D difference gel electrophoresis results (in Bioinformatics 20(13)) Bibliografi Author: Kreil, David P ; Karp, Natasha A. ; Lilley, Kathryn S. Topik: Expression Proteomics; Differential In-Gel Analysis; Normalization; System Bias; Differential Protein Expression; DNA Microarray Bahasa: (EN )    Edisi: Mar 2004     Penerbit: Oxford University Press     Tempat Terbit: London    Tahun Terbit: 2004     Penyerta: http://bioinformatics.oxfordjournals.org/cgi/repri Jenis: Article - diterbitkan di jurnal ilmiah internasional Fulltext: BiasRemoval6sup.pdf (227.67KB; 0 download) 2026.pdf (270.17KB; 0 download) [Informasi yang berkaitan dengan koleksi ini di internet] Abstract Motivation: Two-dimensional Difference Gel Electrophoresis (DIGE) measures expression differences for thousands of proteins in parallel. In contrast to DNA microarray analysis, however, there have been few systematic studies on the validity of differential protein expression analysis, and the effects of normalization methods have not yet been investigated. To address this need, we assessed a series of same–same comparisons, evaluating how random experimental variance influenced differential expression analysis. Results: The strong fluctuations observed were reflected in large discrepancies between the distributions of the spot intensities for different gels. Correct normalization for pooling of multiple gels for analysis is therefore essential. We show that both dye-specific background levels and the differences in scale of the spot intensity distributions must be accounted for. A variance stabilizing transform that had been developed for DNA microarray analysis combined with a robust Z-score allowed the determination of gel-independent signal thresholds based on the empirical distributions from same–same comparisons. In contrast, similar thresholds holding up to cross-validation could not be proposed for data normalized using methods established in the field of proteomics. Kajian editorial Running title: Bias in differential protein expression analysis Opini Anda Klik untuk menuliskan opini Anda tentang koleksi ini! Lihat Sejarah Pengadaan  Konversi Metadata   Kembali

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