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Open Access Software

eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

Wei Zou1, David L Aylor1 and Zhao-Bang Zeng123*

Author Affiliations

1 Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA

2 Department of Statistics, North Carolina State University, Raleigh, NC 27695-7566, USA

3 Department of Genetics, North Carolina State University, Raleigh, NC 27695-7566, USA

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BMC Bioinformatics 2007, 8:7  doi:10.1186/1471-2105-8-7

Published: 9 January 2007

Abstract

Background

Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships between multiple genomic regions and multiple expressional profiles. There is a need for informative bioinformatics tools to assist the visualization and interpretation of these mapping results.

Results

We have developed a web-based tool, called eQTL Viewer, to visualize the relationships between the expression trait genes and the candidate genes in the eQTL regions using Scalable Vector Graphics. The plot generated by eQTL Viewer has the capacity to display mapping results with high resolutions at a variety of scales, and superimpose biological annotations onto the mapping results dynamically.

Conclusion

Our tool provides an efficient and intuitive way for biologists to explore transcriptional regulation patterns, and to generate hypotheses on the genetic basis of transcriptional regulations.