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

Part of the Methods in Molecular Biology book series (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.

Key words

DEG Gene ontology GO terms Essential gene Enrichment analysis 

Notes

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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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of PhysicsTianjin UniversityTianjinChina
  2. 2.Center for Molecular Medicine and Genetics, School of MedicineWayne State UniversityDetroitUSA

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