Functional analysis of the molecular interactions of TATA box-containing genes and essential genes

PloS One
Sang-Hun BaeJisook Moon

Abstract

Genes can be divided into TATA-containing genes and TATA-less genes according to the presence of TATA box elements at promoter regions. TATA-containing genes tend to be stress-responsive, whereas many TATA-less genes are known to be related to cell growth or "housekeeping" functions. In a previous study, we demonstrated that there are striking differences among four gene sets defined by the presence of TATA box (TATA-containing) and essentiality (TATA-less) with respect to number of associated transcription factors, amino acid usage, and functional annotation. Extending this research in yeast, we identified KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways that are statistically enriched in TATA-containing or TATA-less genes and evaluated the possibility that the enriched pathways are related to stress or growth as reflected by the individual functions of the genes involved. According to their enrichment for either of these two gene sets, we sorted KEGG pathways into TATA-containing-gene-enriched pathways (TEPs) and essential-gene-enriched pathways (EEPs). As expected, genes in TEPs and EEPs exhibited opposite results in terms of functional category, transcriptional regulation, codon adaptation index, and network properti...Continue Reading

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Citations

May 4, 2017·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Ertugrul FilizIbrahim Ilker Ozyigit
Feb 6, 2017·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·Recep VatanseverSeckin Eroglu
Jun 11, 2020·Microorganisms·Piyangkun LueangjaroenkitLerluck Chitradon
Aug 13, 2020·Metabolites·Hongting TangJay D Keasling
Dec 14, 2017·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·M Aydın AkbudakKubra Kontbay
May 2, 2021·Trends in Genetics : TIG·Václav BrázdaRichard P Bowater
Aug 10, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Tariq PervaizLingfei Shangguan

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Software Mentioned

Pathview
Cytoscape
MCODE
R
MCDOE
R package
KEGG API

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