Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori.
Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori.
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DOI：
10.1673/031.010.11401
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
Xu SQ
中科院分区：
文献类型：
--
作者：
Gan LP;Zhang WY;Niu YS;Xu L;Xi J;Ji MM;Xu SQ
表达序列标签 (EST) 是转录的 cDNA 序列的短子序列。 EST 代表基因表达，为基因表达分析提供了良好的线索。基于从 NCBI 获得的 EST 数据，开发了 EST 分析包（apEST）。该工具被编程用于 Bombyx mori (L.)（鳞翅目：Bombycidae）的电子表达、蛋白质注释和基因本体 (GO) 类别分析。总共搜索并下载了 FASTA 格式的 245,761 个 EST（截至 2009 年 7 月 1 日），通过运行 apEST 从中提取、分类和汇总组织类型、发育阶段、性别和品系的信息。然后，去除多余部分后形成相应的分布轮廓。获得了不同发育阶段的一种组织以及不同组织的一个发育阶段的基因表达谱。通过运行 apEST 选择看家基因以及组织和阶段特异性基因，与其他两种在线分析方法（SilkDB (BmMDB) 上基于微阵列的基因表达谱和 NCBI 上的 EST 图谱）进行对比。然后将 apEST 运行的过氧化氢酶时空表达谱呈现为三维图，以便直观地可视化模式。从微阵列数据和RT-PCR实验中确认的总共37个查询基因被选为测试apEST的查询。三种方法的结果非常一致。然而，由于调查的项目独特，apEST 和 BmMDB 之间存在细微差别。因此，提出了补充分析。 apEST 的应用还导致获得了 EST 数据集的相应蛋白质注释，并最终获得了其功能。结果根据蛋白质注释和基因本体（GO）类别的统计信息呈现。这些都验证了apEST的可靠性以及该平台的可操作性。 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。
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.
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影响因子：
7
作者：
Ashburner, M;Ball, CA;Yoon, J
通讯作者：
Yoon, J
微阵列和 EST 数据库对 mRNA 表达水平的估计不同：：C-elegans 的蛋白质长度与表达曲线--：第 30 条。 30
影响因子：
4.4
作者：
Munoz, ET;Bogarad, LD;Deem, MW
通讯作者：
Deem, MW
影响因子：
7
作者：
Lash, AE;Tolstoshev, CM;Altschul, SF
通讯作者：
Altschul, SF
影响因子：
5.8
作者：
Su, Y;Murali, TM;Kasif, S
通讯作者：
Kasif, S
影响因子：
0.9
作者：
Hong, Sun-Mee;Nho, Si-Kab;Kang, Seok-Woo
通讯作者：
Kang, Seok-Woo