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Open Access Data Note

EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli

Xiao Chang14, Yun Li12, Jie Ping3, Xiao-Bin Xing12, Han Sun12, Peng Jia12, Chuan Wang12, Yuan-Yuan Li12* and Yi-Xue Li123*

Author Affiliations

1 Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China

2 Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China

3 College of life science and biotechnology, Shanghai Jiaotong University, Shanghai 200120, China

4 Zilkha Neurogenetic Institute, Department of Psychiatry and Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA

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BMC Research Notes 2011, 4:405  doi:10.1186/1756-0500-4-405

Published: 13 October 2011

Abstract

Background

Escherichia coli has been extensively studied as a prokaryotic model organism whose whole genome was determined in 1997. However, it is difficult to identify all the gene products involved in diverse functions by using whole genome sequencesalone. The high-resolution transcriptome mapping using tiling arrays has proved effective to improve the annotation of transcript units and discover new transcripts of ncRNAs. While abundant tiling array data have been generated, the lack of appropriate visualization tools to accommodate and integrate multiple sources of data has emerged.

Findings

EcoBrowser is a web-based tool for visualizing genome annotations and transcriptome data of E. coli. Important tiling array data of E. coli from different experimental platforms are collected and processed for query. An AJAX based genome browser is embedded for visualization. Thus, genome annotations can be compared with transcript profiling and genome occupancy profiling from independent experiments, which will be helpful in discovering new transcripts including novel mRNAs and ncRNAs, generating a detailed description of the transcription unit architecture, further providing clues for investigation of prokaryotic transcriptional regulation that has proved to be far more complex than previously thought.

Conclusions

With the help of EcoBrowser, users can get a systemic view both from the vertical and parallel sides, as well as inspirations for the design of new experiments which will expand our understanding of the regulation mechanism.