National Engineering Laboratory for Modem Silk, Department of Applied Biology, Medical College of Soochow University, Suzhou, 215153, P. R. China.
J Insect Sci. 2010;10:114. doi: 10.1673/031.010.11401.
An Expressed Sequence Tag (EST) is a short sub-sequence of a transcribed cDNA sequence. ESTs represent gene expression and give good clues for gene expression analysis. Based on EST data obtained from NCBI, an EST analysis package was developed (apEST). This tool was programmed for electronic expression, protein annotation and Gene Ontology (GO) category analysis in Bombyx mori (L.) (Lepidoptera: Bombycidae). A total of 245,761 ESTs (as of 01 July 2009) were searched and downloaded in FASTA format, from which information for tissue type, development stage, sex and strain were extracted, classified and summed by running apEST. Then, corresponding distribution profiles were formed after redundant parts had been removed. Gene expression profiles for one tissue of different developmental stages and from one development stage of the different tissues were attained. A housekeeping gene and tissue-and-stage-specific genes were selected by running apEST, contrasting with two other online analysis approaches, microarray-based gene expression profile on SilkDB (BmMDB) and EST profile on NCBI. A spatio-temporal expression profile of catalase run by apEST was then presented as a three-dimensional graph for the intuitive visualization of patterns. A total of 37 query genes confirmed from microarray data and RT-PCR experiments were selected as queries to test apEST. The results had great conformity among three approaches. Nevertheless, there were minor differences between apEST and BmMDB because of the unique items investigated. Therefore, complementary analysis was proposed. Application of apEST also led to the acquisition of corresponding protein annotations for EST datasets and eventually for their functions. The results were presented according to statistical information on protein annotation and Gene Ontology (GO) category. These all verified the reliability of apEST and the operability of this platform. The apEST can also be applied in other species by modifying some parameters and serves as a model for gene expression study for Lepidoptera.
表达序列标签 (EST) 是转录 cDNA 序列的短亚序列。EST 代表基因表达，为基因表达分析提供了很好的线索。基于从 NCBI 获得的 EST 数据，开发了一个 EST 分析包 (apEST)。该工具用于电子表达、蛋白质注释和基因本体论 (GO) 类别分析在 Bombyx mori (L.) (鳞翅目: Bombycidae)。截至 2009 年 7 月 1 日，共搜索并以 FASTA 格式下载了 245,761 个 EST，通过运行 apEST 提取、分类和汇总组织类型、发育阶段、性别和菌株的信息。然后，去除冗余部分后形成相应的分布图谱。获得了不同发育阶段同一组织和不同组织同一发育阶段的基因表达图谱。通过运行 apEST，选择管家基因和组织-阶段特异性基因，并与 SilkDB (BmMDB)上的基于微阵列的基因表达谱和 NCBI 上的 EST 谱进行对比。然后通过 apEST 呈现了一个过氧化氢酶的时空表达图谱作为一个三维图，用于直观地可视化模式。从微阵列数据和 RT-PCR 实验中总共选择了 37 个查询基因作为查询来测试 apEST。三种方法的结果具有很大的一致性。然而，由于所研究的独特项目，apEST 和 BmMDB 之间存在一些微小的差异。因此，提出了互补分析。apEST 的应用还为 EST 数据集及其功能获得了相应的蛋白质注释。结果根据蛋白质注释和基因本体论 (GO) 类别的统计信息呈现。所有这些都验证了 apEST 的可靠性和该平台的可操作性。apEST 还可以通过修改一些参数应用于其他物种，并作为鳞翅目基因表达研究的模型。
