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Contents 1

Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes / Shibsankar Das ; Brajadulal Chottopadhyay ; Satyabrata Sahoo 1

[요약] 1

Introduction 1

Methods 2

Results and Discussion 4

References 9

초록보기

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS.

Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

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Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes Shibsankar Das, Brajadulal Chottopadhyay, Satyabrata Sahoo pp.38-47

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참고문헌 (38건) : 자료제공( 네이버학술정보 )

참고문헌 목록에 대한 테이블로 번호, 참고문헌, 국회도서관 소장유무로 구성되어 있습니다.
번호 참고문헌 국회도서관 소장유무
1 Codon bias and heterologous protein expression 네이버 미소장
2 Major codon preference: theme and variations. 네이버 미소장
3 Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. 네이버 미소장
4 Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. 네이버 미소장
5 Downregulating viral gene expression: codon usage bias manipulation for the generation of novel influenza A virus vaccines. 네이버 미소장
6 Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. 네이버 미소장
7 Selection intensity for codon bias. 네이버 미소장
8 Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. 네이버 미소장
9 Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes 네이버 미소장
10 Codon usage and tRNA content in unicellular and multicellular organisms. 네이버 미소장
11 Predicted highly expressed genes of diverse prokaryotic genomes. 네이버 미소장
12 Predicted Highly Expressed Genes in Archaeal Genomes 네이버 미소장
13 Codon bias signatures, organization of microorganisms in codon space, and lifestyle. 네이버 미소장
14 Codon bias and gene expression 네이버 미소장
15 Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity 네이버 미소장
16 Correction of sequencing errors in a mixed set of reads 네이버 미소장
17 The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications 네이버 미소장
18 Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression 네이버 미소장
19 Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome 네이버 미소장
20 Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance. 네이버 미소장
21 Gene expression profile of the cynobacterium synechocystis genome. 네이버 미소장
22 Relative codon adaptation index, a sensitive measure of codon usage bias. 네이버 미소장
23 Quantifying Position-Dependent Codon Usage Bias 네이버 미소장
24 Analyzing Gene Expression and Codon Usage Bias in Diverse Genomes Using a Variety of Models 네이버 미소장
25 Sahoo S, Das S. Analyzing gene expression and codon usage bias in Metallosphaera sedula. J Bioinform Intell Control 2014;3:72-80. 미소장
26 Amils R. Crenarchaeota. In: Encyclopedia of Astrobiology (Amils R, Gargaud M, Cernicharo Quintanilla J, Cleaves HJ, Irvine WM, Pinti D, et al., eds.). Berlin: Springer-Verlag, 2011. p. 390. 미소장
27 Thermophilic microorganisms in biomining 네이버 미소장
28 In vitro Uses of Biological Cryoprotectants 네이버 미소장
29 Hypothermic protection — A fundamental property of “Antifreeze” proteins 네이버 미소장
30 Perspectives on Archaeal Diversity, Thermophily and Monophyly from Environmental rRNA Sequences 네이버 미소장
31 Switches in species-specific codon preferences: the influence of mutation biases. 네이버 미소장
32 A new measure to study phylogenetic relations in the brown algal order Ectocarpales: the "codon impact parameter". 네이버 미소장
33 Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes 네이버 미소장
34 Synonymous codon usage is subject to selection in thermophilic bacteria 네이버 미소장
35 On the Genetic Basis of Variation and Heterogeneity of DNA Base Composition 네이버 미소장
36 An Archaeal Genomic Signature 네이버 미소장
37 Protein domains of unknown function are essential in bacteria. 네이버 미소장
38 Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis. 네이버 미소장

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