Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues
Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues
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DOI：
10.1093/nar/27.21.4251
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发表时间：
1999-11-01
影响因子：
14.9
通讯作者：
Rosenthal, A
中科院分区：
文献类型：
--
作者：
Schmitt, AO;Specht, T;Rosenthal, A
本文介绍了一种高效、系统地挖掘整个EST文库中差异表达基因的四步法。第一步，从所研究的EST文库中去除冗余条目；第二步，利用约400万个公共和专有EST，在剩余的每个EST基础上构建最长的重叠群；第三步，将这些推定基因与一个包含来自16种不同组织（正常组织和肿瘤组织）的EST的数据库进行比对，以确定它们是否差异表达（第三步；电子Northern杂交）。采用费舍尔精确检验来评估差异表达的显著性。第四步，尝试通过数据库比对来描述组装过程中获得的重叠群的特征。对CGAP文库NCI_CGAP_Br1.1进行了案例研究，该文库由三种（高分化、中分化和低分化）浸润性导管乳腺癌肿瘤构建而成（共2126个EST）。在最长的重叠群中，发现有139个在乳腺肿瘤组织中显著（α = 0.05）过表达，而有13个似乎是下调的。
A four-step procedure for the efficient and systematic mining of whole EST libraries for differentially expressed genes is presented. After eliminating redundant entries from the EST library under investigation (step 1), contigs of maximal length are built upon each remaining EST using about 4000000 public and proprietary ESTs (step 2), These putative genes are compared against a database comprising ESTs from 16 different tissues (both normal and tumour affected) to determine whether or not they are differentially expressed (step 3; electronic northern). Fisher's exact test is used to assess the significance of differential expression. In step 4, an attempt is made to characterise the contigs obtained in the assembly through database comparison. A case study of the CGAP library NCI_CGAP_Br1.1, a library made from three (well, moderately, and poorly differentiated) invasive ductal breast tumours (2126 ESTs in total) was carried out. Of the maximal contigs, 139 were found to be significantly (alpha = 0.05) overexpressed in breast tumour tissue, while 13 appeared to be down-regulated.