Protocol

Microbial Gene Essentiality: Protocols and Bioinformatics

Volume 416 of the series Methods in Molecular Biology™ pp 391-400

Gene Essentiality Analysis Based on DEG, a Database of Essential Genes

  • Chun-Ting ZhangAffiliated withDepartment of Physics, Tianjin University
  • , Ren ZhangAffiliated withDepartment of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital

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Abstract

Essential genes are the genes that are indispensable for the survival of an organism. The genome-scale identification of essential genes has been performed in various organisms, and we consequently constructed DEG, a Database that contains currently available essential genes. Here we analyzed functional distributions of essential genes in DEG, and found that some essential-gene functions are even conserved between the prokaryote (bacteria) and the eukaryote (yeast), e.g., genes involved in information storage and processing are overrepresented, whereas those involved in metabolism are underrepresented in essential genes compared with non-essential ones. In bacteria, species specificity in functional distribution of essential genes is mainly due to those involved in cellular processes. Furthermore, within the category of information storage and processing, function of translation, ribosomal structure, and biogenesis are predominant in essential genes. Finally, some potential pitfalls for analyzing gene essentiality based on DEG are discussed.

Key Words

COG database DEG essential gene