A non-EST-based method for exon-skipping prediction
A non-EST-based method for exon-skipping prediction
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DOI：
10.1101/gr.2572604
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发表时间：
2004-08-01
期刊：
影响因子：
7
通讯作者：
Shamir, R
中科院分区：
文献类型：
--
作者：
Sorek, R;Shemesh, R;Shamir, R
据估计，35%至74%的人类基因可以进行选择性剪接。目前，大规模检测可变剪接最有效的方法是使用表达序列标签（EST）或微阵列分析。由于这些方法仅对转录组进行采样，因此未出现在深度采样组织中的剪接变体被检测到的概率较低。我们提出了一种新的方法，通过该方法，我们可以预测一个内部外显子被跳过（即它是否是一个盒式外显子），仅仅基于它的裸基因组序列和油的序列，其小鼠直系同源物。预测不需要其他数据，如EST。使用我们的方法，这是实验验证，我们检测到数百个新的剪接变异，无法检测到使用EST。我们发现，人类基因组中的剪接变异体的相当大的一部分不能通过目前的人类EST或cDNA数据进行鉴定。
It is estimated that between 35% and 74% of all human genes can undergo alternative splicing. Currently, the most efficient methods for large-scale detection of alternative splicing use expressed sequence tags (ESTs) or microarray analysis. As these methods merely sample the transcriptome, splice variants that do not appear in deeply sampled tissues have a low probability of being detected. We present a new method by which we can predict that an internal exon is skipped (namely whether it is a cassette-exon) merely based on its naked genomic sequence and oil the sequence of its mouse ortholog. No other data, Such as ESTs, are required for the prediction. Using our method, which was experimentally validated, we detected hundreds of novel splice variants that were not detectable using ESTs. We show that a Substantial fraction of the splice variants in the human genome Could not be identified through Current human EST or cDNA data.