Discovery of tissue-specific exons using comprehensive human exon microarrays.
Discovery of tissue-specific exons using comprehensive human exon microarrays.
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DOI：
10.1186/gb-2007-8-4-r64
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Blume JE
中科院分区：
文献类型：
--
作者：
Clark TA;Schweitzer AC;Chen TX;Staples MK;Lu G;Wang H;Williams A;Blume JE
使用具有简单基因内标准化算法的综合外显子微阵列来检测人类组织特异性选择性剪接事件，表明已知外显子和注释良好的基因之外的显着表达以及高频率的选择性剪接事件。高等真核生物表达通过选择性剪接产生的多种信使 RNA。监测基因表达的大规模方法必须进行调整，以便准确检测这种剪接产生的转录本变异。我们设计了一种高密度寡核苷酸微阵列，其探针组用于人类基因组中超过一百万个注释和预测的外显子。使用这些阵列和将外显子信号标准化为整个基因信号的简单算法，我们从一组 16 种不同的正常成人组织中鉴定出了组织特异性外显子。 RT-PCR 验证证实了大约 86% 的预测组织富集探针组。组织之间的成对比较表明，多达 73% 的检测到的基因存在差异性选择性剪接。我们还演示了如何使用包容性外显子微阵列来发现新的选择性剪接事件。例如，来自 11 个基因的 17 个新的组织特异性外显子通过 RT-PCR 和测序进行了验证。结合概念上简单的算法，综合外显子微阵列可以检测组织特异性的选择性剪接事件。我们的数据表明已知外显子和注释良好的基因之外的显着表达以及高频率的选择性剪接事件。此外，我们还鉴定并验证了许多具有组织特异性剪接模式的新型外显子。组织图谱数据可能会成为有关选择性剪接调控的宝贵信息来源。
Comprehensive exon microarrays with a simple intra-gene normalization algorithm were used to detect human tissue-specific alternative splicing events, suggesting significant expression outside of known exons and well annotated genes and a high frequency of alternative splicing events. Higher eukaryotes express a diverse population of messenger RNAs generated by alternative splicing. Large-scale methods for monitoring gene expression must adapt in order to accurately detect the transcript variation generated by this splicing. We have designed a high-density oligonucleotide microarray with probesets for more than one million annotated and predicted exons in the human genome. Using these arrays and a simple algorithm that normalizes exon signal to signal from the gene as a whole, we have identified tissue-specific exons from a panel of 16 different normal adult tissues. RT-PCR validation confirms approximately 86% of the predicted tissue-enriched probesets. Pair-wise comparisons between the tissues suggest that as many as 73% of detected genes are differentially alternatively spliced. We also demonstrate how an inclusive exon microarray can be used to discover novel alternative splicing events. As examples, 17 new tissue-specific exons from 11 genes were validated by RT-PCR and sequencing. In conjunction with a conceptually simple algorithm, comprehensive exon microarrays can detect tissue-specific alternative splicing events. Our data suggest significant expression outside of known exons and well annotated genes and a high frequency of alternative splicing events. In addition, we identified and validated a number of novel exons with tissue-specific splicing patterns. The tissue map data will likely serve as a valuable source of information on the regulation of alternative splicing.
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DOI：
10.1073/pnas.1534744100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Mei, R;Hubbell, E;Webster, TA
通讯作者：
Webster, TA
影响因子：
56.9
作者：
Cheng, J;Kapranov, P;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
4.4
作者：
Gupta S;Zink D;Korn B;Vingron M;Haas SA
通讯作者：
Haas SA
影响因子：
10.6
作者：
Lee, CJ;Irizarry, K
通讯作者：
Irizarry, K
影响因子：
30.8
作者：
Frey, BJ;Mohammad, N;Hughes, TR
通讯作者：
Hughes, TR