Nagpal Shailender, Karaman Mazen W, Timmerman Michelle M, Ho Vincent V, Pike Brian L, Hacia Joseph G
The Institute for Genetic Medicine, University of Southern California, 2250 Alcazar Street, IGM 240, Los Angeles, CA 90089, USA.
Nucleic Acids Res. 2004 Mar 18;32(5):e51. doi: 10.1093/nar/gnh048.
DNA microarrays are powerful tools for comparing gene expression profiles from closely related organisms. However, a single microarray design is frequently used in these studies. Therefore, the levels of certain transcripts can be grossly underestimated due to sequence differences between the transcripts and the arrayed DNA probes. Here, we seek to improve the sensitivity and specificity of oligonucleotide microarray-based gene expression analysis by using genomic sequence information to predict the hybridization efficiency of orthologous transcripts to a given microarray. To test our approach, we examine hybridization patterns from three Escherichia coli strains on E.coli K-12 MG1655 gene expression microarrays. We create electronic mask files to discard data from probes predicted to have poor hybridization sensitivity and specificity to cDNA targets from each strain. We increased the accuracy of gene expression analysis and identified genes that cannot be accurately interrogated in each strain using these microarrays. Overall, these studies provide guidelines for designing effective electronic masks for gene expression analysis in organisms where substantial genome sequence information is available.
DNA微阵列是用于比较密切相关生物体基因表达谱的强大工具。然而，这些研究中经常使用单一的微阵列设计。因此，由于转录本与阵列DNA探针之间的序列差异，某些转录本的水平可能会被严重低估。在这里，我们试图通过利用基因组序列信息来预测直系同源转录本与给定微阵列的杂交效率，以提高基于寡核苷酸微阵列的基因表达分析的灵敏度和特异性。为了测试我们的方法，我们检测了三种大肠杆菌菌株在大肠杆菌K-12 MG1655基因表达微阵列上的杂交模式。我们创建了电子掩码文件，以丢弃那些预测对各菌株cDNA靶标具有较差杂交灵敏度和特异性的探针的数据。我们提高了基因表达分析的准确性，并鉴定出使用这些微阵列无法在每个菌株中准确检测的基因。总体而言，这些研究为在有大量基因组序列信息的生物体中设计用于基因表达分析的有效电子掩码提供了指导。
