Survey of allelic expression using EST mining
Survey of allelic expression using EST mining
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DOI：
10.1101/gr.4023805
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发表时间：
2005-11-01
期刊：
影响因子：
7
通讯作者：
Pastinen, T
中科院分区：
文献类型：
--
作者：
Ge, B;Gurd, S;Pastinen, T
基因调控中的顺式作用等位基因变异是表型变异的来源。因此，最近的研究通过实验筛选了人类基因，试图启动具有顺式作用变体的基因目录。在本研究中，我们使用dbEST中的人类EST数据作为等位基因表达数据的来源，并使用HapMap数据库来提供人群中预期的等位基因频率。我们证明，与在亚洲和非洲获得的人口样本相比，从 dbEST 中的人类 EST 估计的等位基因频率与来自代表北欧和西欧白种人的 CEPH HapMap 样本的等位基因频率具有更大的一致性。 EST 数据库中观察到的等位基因频率与从 CEPH HapMap 样本中获得的等位基因频率之间的偏差可能是由于常见的可遗传顺式作用变异改变了 RNA 中的相对等位基因分布所致。我们提供了计算机模拟和实验证据，表明该策略确实允许显着富集具有与表达等位基因连锁不平衡的常见可遗传顺式作用多态性的基因。
Cis-acting allelic variation in gene regulation is a source of phenotypic variation. Consequently, recent studies have experimentally screened human genes in an attempt to initiate a catalog of genes possessing cis-acting variants. In this study, we use human EST data in dbEST as the source of allelic expression data, and the HapMap database to provide expected allele frequencies in human populations. We demonstrate a greater concordance of allele frequencies estimated from human ESTs in dbEST with those derived from the CEPH HapMap sample representing Caucasians from northern and western Europe, than population samples obtained in Asia and Africa. Deviations between allele frequencies observed in EST databases and the ones obtained from the CEPH HapMap samples may result from common heritable cis-acting variants altering the relative allele distribution in RNA. We provide in silico as well as experimental evidence that this strategy does allow significant enrichment of genes harboring common heritable cis-acting polymorphisms in linkage disequilibrium with expressed alleles.