Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori

Li- Ping Gan1,2a, Wen-Yu Zhang3b, Yan-Shan Niu1c, Li Xu1d, Jian Xi1e , Ming-Ming Ji1f, and Shi-Qing Xu1g*

1National Engineering Laboratory for Modern Silk, Department of Applied Biology, Medical College of Soochow University, Suzhou, 215153, P. R. China
2Biology Department, Chongqing Three Gorges University, Chongqing, 404000, China
3Bioinformatics Department, Medical College, Soochow University, Suzhou, 215153, China

Abstract

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-andstage- 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.

Keywords: EST analysis package, UniGene, Lepidoptera
Abbreviations: EST, Expressed Sequence Tag; apEST, EST analysis package; dbEST, database EST; GO, Gene Ontology; TPM, transcripts per million; BmMDB, Microarray-based gene expression profile on SilkDB; MSG, middle silkgland; PSG, posterior silkgland

Correspondence: aganmei790717@163.com, bmichael_0214@126.com, cdushuhuniu@hotmail.com, dxulisd@sina.com, e13771956726@139.com, fsudajmm@yahoo.com.cn, g*szsqxu@suda.edu.cn, *Corresponding author
Associate Editor: Brad Coates was editor of this paper.

Received: 1 September 2009 | Accepted: 25 January 2010 | Published: 23 July 2010

ISSN: 1536-2442 | Volume 10, Number 114

Gan LP, Zhang WY, Niu YS, Xu L, Xi J, Ji MM, Xu SQ. 2010. Construction and application of an electronic spatiotemporal expression profile and gene ontology analysis platform based on the EST database of the silkworm, Bombyx mori. Journal of Insect Science 10:114, available online: insectscience.org/10.114


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