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Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes

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Gene Essentiality

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1279))

Abstract

The database of essential genes (DEG, available at http://www.essentialgene.org), constructed in 2003, has been timely updated to harbor essential-gene records of bacteria, archaea, and eukaryotes. DEG 10, the current release, includes not only essential protein-coding genes determined by genome-wide gene essentiality screens but also essential noncoding RNAs, promoters, regulatory sequences, and replication origins. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools. Based on the analysis of DEG 10, we show that the percentage of essential genes in bacterial genomes exhibits an exponential decay with increasing genome sizes. The functions, ATP binding (GO:0005524), GTP binding (GO:0005525), and DNA-directed RNA polymerase activity (GO:0003899), are likely required for organisms across life domains.

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Acknowledgements

The present work was supported in part by a startup fund from Wayne State University to R.Z., the National Natural Science Foundation of China (Grant Nos. 31171238 and 30800642 to F.G. and 90408028 to C.T.Z.), and Program for New Century Excellent Talents in University (No. NCET-12-0396) to F.G.

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Authors and Affiliations

  1. Department of Physics, Tianjin University, Tianjin, 300072, China

    Feng Gao, Hao Luo & Chun-Ting Zhang

  2. Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, 3319 Scott Hall, 540 East Canfield Street, Detroit, MI, 48201, USA

    Ren Zhang

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  1. Feng Gao
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  2. Hao Luo
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  3. Chun-Ting Zhang
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  4. Ren Zhang
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Correspondence to Ren Zhang .

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Editors and Affiliations

  1. Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA

    Long Jason Lu

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Gao, F., Luo, H., Zhang, CT., Zhang, R. (2015). Gene Essentiality Analysis Based on DEG 10, an Updated Database of Essential Genes. In: Lu, L. (eds) Gene Essentiality. Methods in Molecular Biology, vol 1279. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2398-4_14

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  • DOI: https://doi.org/10.1007/978-1-4939-2398-4_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2397-7

  • Online ISBN: 978-1-4939-2398-4

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