Dataset Information

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

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.

SUBMITTER: Xu G

PROVIDER: S-EPMC3680244 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Publications

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

Xu Guangyu G Liu Bin B Wang Fang F Wei Chengguo C Zhang Ying Y Sheng Jiyao J Wang Guoqing G Li Fan F

BMC infectious diseases 20130520

<h4>Background</h4>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 ...[more]

PMID: 23687949

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Project description:BackgroundMycobacterium tuberculosis is one of the deadliest pathogens in humans. Co-infection of M. tuberculosis with HIV and the emergence of multi-drug-resistant tuberculosis (TB) constitute a serious global threat. However, no effective anti-TB drugs are available, with the exception of first-line drugs such as isoniazid. The cell wall of M. tuberculosis, which is primarily responsible for the lack of effective anti-TB drugs and the escape of the bacteria from host immunity, is an important drug target. The core components of the cell wall of M. tuberculosis are peptidoglycan, arabinogalactan, and mycotic acid. However, the functional genome and metabolic regulation pathways for the M. tuberculosis cell wall are still unknown. In this study, we used the biclustering algorithm integrated into cMonkey, sequence alignment, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other bioinformatics methods to scan the whole genome of M. tuberculosis as well as to identify and statistically analyze the genes related to the synthesis of the M. tuberculosis cell wall.MethodWe performed high-throughput genome-wide screening for M. tuberculosis using Biocarta, KEGG, National Cancer Institute Pathway Interaction Database (NCI-PID), HumanCyc, and Reactome. We then used the Database of Origin and Registration (DOOR) established in our laboratory to classify the collection of operons for M. tuberculosis cell wall synthetic genes. We used the cMonkey double clustering algorithm to perform clustering analysis on the gene expression profile of M. tuberculosis for cell wall synthesis. Finally, we visualized the results using Cytoscape.Result and conclusionThrough bioinformatics and statistical analyses, we identified 893 M. tuberculosis H37Rv cell wall synthesis genes, distributed in 20 pathways, involved in 46 different functions related to cell wall synthesis, and clustered in 386 modules. We identified important pivotal genes and proteins in the cell wall synthesis pathway such as murA, a class of operons containing genes involved in cell wall synthesis such as ID6951, and a class of operons indispensable for the survival of the bacteria. In addition, we found 41 co-regulatory modules for cell wall synthesis and five co-expression networks of molecular complexes involved in peptidoglycan biosynthesis, membrane transporter synthesis, and other cell wall processes.

Dataset Information

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

Background

Method

Results

Conclusion

Publications

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

Similar Datasets

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