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Open Access Correspondence

High-throughput screen of essential gene modules in Mycobacterium tuberculosis: a bibliometric approach

Guangyu Xu1, Bin Liu2, Fang Wang1, Chengguo Wei1, Ying Zhang1, Jiyao Sheng1, Guoqing Wang1* and Fan Li1*

Author Affiliations

1 Key Laboratory of Zoonosis, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, China

2 The First Bethune Hospital of Jilin University, Changchun, Jilin, China

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BMC Infectious Diseases 2013, 13:227  doi:10.1186/1471-2334-13-227

Published: 20 May 2013

Abstract

Background

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). The annotation of functional genome and signaling network in M. tuberculosis are still not systematic. Essential gene modules are a collection of functionally related essential genes in the same signaling or metabolic pathway. The determination of essential genes and essential gene modules at genomic level may be important for better understanding of the physiology and pathology of M. tuberculosis, and also helpful for the development of drugs against this pathogen. The establishment of genomic operon database (DOOR) and the annotation of gene pathways have felicitated the genomic analysis of the essential gene modules of M. tuberculosis.

Method

Bibliometric approach has been used to perform a High-throughput screen for essential genes of M. tuberculosis strain H37Rv. Ant colony algorithm were used to identify the essential genes in other M. tuberculosis reference strains. Essential gene modules were analyzed by operon database DOOR. The pathways of essential genes were assessed by Biocarta, KEGG, NCI-PID, HumanCyc and Reactome. The function prediction of essential genes was analyzed by Pfam.

Results

A total approximately 700 essential genes were identified in M. tuberculosis genome. 40% of operons are consisted of two or more essential genes. The essential genes were distributed in 92 pathways in M. tuberculosis. In function prediction, 61.79% of essential genes were categorized into virulence, intermediary metabolism/respiration,cell wall related and lipid metabolism, which are fundamental functions that exist in most bacteria species.

Conclusion

We have identified the essential genes of M. tuberculosis using bibliometric approach at genomic level. The essential gene modules were further identified and analyzed.

Keywords:
Mycobacterium tuberculosis; Essential gene modules; Operon; Pathway