Gene Prioritization of Resistant Rice Gene againstXanthomas oryzae pv. oryzaeby Using Text Mining Technologies

Jingbo Xia,Daojun Yuan,Alex Chengyu Fang,Jonathan Webster,Xing Zhang,Lingling Chen

doi:10.1155/2013/853043

Abstract

To effectively assess the possibility of the unknown rice protein resistant to Xanthomonas oryzae pv. oryzae, a hybrid strategy is proposed to enhance gene prioritization by combining text mining technologies with a sequence-based approach. The text mining technique of term frequency inverse document frequency is used to measure the importance of distinguished terms which reflect biomedical activity in rice before candidate genes are screened and vital terms are produced. Afterwards, a built-in classifier under the chaos games representation algorithm is used to sieve the best possible candidate gene. Our experiment results show that the combination of these two methods achieves enhanced gene prioritization.

Highlights

Due to the availability of abundant genomic resources, rice has become a model species for the genomic study
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a worldwide devastating disease, which is second only to the Pyricularia grisea, and causes yield losses ranging from 20% to 30%, and in some areas of Asia the loss can be as high as 50% [2]
The results demonstrate that spatial gene expression patterns have been successfully exploited to predict gene-phenotype associations for both mouse phenotypes and human central nervous system-related Mendelian disorders

Summary

Introduction

Due to the availability of abundant genomic resources, rice has become a model species for the genomic study. Bacterial blight, caused by Xanthomonas oryzae pv. Oryzae (Xoo), is a worldwide devastating disease, which is second only to the Pyricularia grisea, and causes yield losses ranging from 20% to 30%, and in some areas of Asia the loss can be as high as 50% [2]. Bacterial blight resistance genes have been cloned by a map-based cloning approach. Thirty bacterial blight resistance genes in rice have been identified. Six genes, namely, Xa1, Xa5, Xa13, Xa21, Xa3/Xa26, and Xa27, have been reported to be isolated for bacterial blight resistance [3,4,5,6]. While on one hand the results of resistant gene discovery with map-based cloning approach are accurate, these laboratory experiments take years of endeavor and a huge amount of input in terms of human and material resources. It is important to find a more effective way to locate vital resistant genes

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Results

Conclusion