Huminiecki L, Bicknell R
Molecular Angiogenesis Laboratory, Imperial Cancer Research Fund, Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
Genome Res. 2000 Nov;10(11):1796-806. doi: 10.1101/gr.150700.
The endothelium plays a pivotal role in many physiological and pathological processes and is known to be an exceptionally active transcriptional site. To advance our understanding of endothelial cell biology and to elucidate potential pharmaceutical targets, we developed a new database screening approach to permit identification of novel endothelial-specific genes. The UniGene gene index was screened using high stringency BLAST against a pool of endothelial expressed sequence tags (ESTs) and a pool of nonendothelial ESTs constructed from cell-type-specific dbEST libraries. UniGene clusters with matches in the endothelial pool and no matches in the nonendothelial pool were selected. The UniGene/EST approach was then combined with serial analysis of gene expression (SAGE) library subtraction and reverse transcription polymerase chain reaction to further examine interesting clusters. Four novel genes were identified and labeled: endothelial cell-specific molecules (ECSM) 1-3 and magic roundabout (similar to the axon guidance protein roundabout). In summary, we present a powerful novel approach for comparative expression analysis combining two datamining strategies followed by experimental verification.
内皮细胞在许多生理和病理过程中发挥着关键作用，并且已知是一个异常活跃的转录位点。为了增进我们对内皮细胞生物学的理解并阐明潜在的药物靶点，我们开发了一种新的数据库筛选方法，以鉴定新的内皮细胞特异性基因。使用高严格度的BLAST，针对由细胞类型特异性dbEST文库构建的内皮细胞表达序列标签（EST）库和非内皮细胞EST库，对UniGene基因索引进行筛选。选择在内皮细胞库中有匹配而在非内皮细胞库中无匹配的UniGene簇。然后将UniGene/EST方法与基因表达系列分析（SAGE）文库消减和逆转录聚合酶链反应相结合，以进一步研究感兴趣的簇。鉴定并标记了四个新基因：内皮细胞特异性分子（ECSM）1 - 3和神奇环行蛋白（类似于轴突导向蛋白环行蛋白）。总之，我们提出了一种强大的新方法，用于结合两种数据挖掘策略并进行实验验证的比较表达分析。
