Predicting splice variant from DNA chip expression data
Predicting splice variant from DNA chip expression data
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DOI：
10.1101/gr.165501
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发表时间：
2001-07-01
期刊：
影响因子：
7
通讯作者：
Wang, YX
中科院分区：
文献类型：
--
作者：
Hu, GK;Madore, SJ;Wang, YX
前信使RNA的选择性剪接是真核基因表达的重要调控层。大量基因的剪接变异参与了细胞的各种生长和分化过程。为了大规模测量特定组织的基因剪接，我们收集了11个大鼠组织的基因表达数据，使用代表1600个大鼠基因的高密度寡核苷酸阵列。芯片上每个基因的表达由20对独立的寡核苷酸探针测量。为了在单个寡核苷酸探针水平对不同组织之间的芯片杂交信号进行归一化和比较，已经开发了两种算法。通过算法识别检测潜在组织特异性剪接变体的寡核苷酸探针(每个探针对的完美匹配[PM]探针)。识别的候选剪接变异体已经与EST聚类程序预测的选择性剪接转录本进行了比较。此外，通过RT-PCR实验验证了算法预测的候选候选中有50%是正确的。研究表明，基于寡核苷酸探针的DNA芯片分析为在基因组水平上检测剪接变体提供了一种强有力的方法。
Alternative splicing of premessenger RNA is an important layer of regulation in eukaryotic gene expression. Splice variation of a large number of genes has been implicated in various cell growth and differentiation processes. To measure tissue-specific splicing of genes on a large scale, we collected gene expression data from 11 rat tissues using a high-density oligonucleotide array representing 1600 rat genes. Expression of each gene on the chip is measured by 20 pairs of independent oligonucleotide probes. Two algorithms have been developed to normalize and compare the chip hybridization signals among different tissues at individual oligonucleotide probe level. Oligonucleotide probes (the perfect match [PM] probe of each probe pair), detecting potential tissue-specific splice variants, were identified by the algorithms. The identified candidate splice variants have been compared to the alternatively spliced transcripts predicted by an EST clustering program. In addition, 50% of the top candidates predicted by the algorithms were confirmed by RT-PCR experiment. The study indicates that oligonucleotide probe-based DNA chip assays provide a powerful approach to detect splice variants at genome scale.