Cluster analysis of the codon use frequency of MHC genes from different species

Jianmin Ma; Tong Zhou; Wanjun Gu; Xiao Sun; Zuhong Lu

doi:10.1016/S0303-2647(02)00016-3

Cluster analysis of the codon use frequency of MHC genes from different species

Jianmin Ma, Tong Zhou, Wanjun Gu, Xiao Sun, Zuhong Lu

Research output: Contribution to journal › Article › peer-review

54 Scopus citations

Abstract

The relative synonymous codon use frequency of 135 MHC genes from four mammal species (Homo sapiens, Pan troglodyte, Macaca mulanta and Rattus norvegicus) is analyzed using a hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions. The conclusion may be useful in gene classification and gene function prediction.

Original language	English (US)
Pages (from-to)	199-207
Number of pages	9
Journal	BioSystems
Volume	65
Issue number	2-3
DOIs	https://doi.org/10.1016/S0303-2647(02)00016-3
State	Published - 2002
Externally published	Yes

Keywords

Codon usage bias
Hierarchical cluster analysis
MHC
Relative synonymous codon use frequency (RSCU)

ASJC Scopus subject areas

Statistics and Probability
Modeling and Simulation
General Biochemistry, Genetics and Molecular Biology
Applied Mathematics

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10.1016/S0303-2647(02)00016-3

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title = "Cluster analysis of the codon use frequency of MHC genes from different species",

abstract = "The relative synonymous codon use frequency of 135 MHC genes from four mammal species (Homo sapiens, Pan troglodyte, Macaca mulanta and Rattus norvegicus) is analyzed using a hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions. The conclusion may be useful in gene classification and gene function prediction.",

keywords = "Codon usage bias, Hierarchical cluster analysis, MHC, Relative synonymous codon use frequency (RSCU)",

author = "Jianmin Ma and Tong Zhou and Wanjun Gu and Xiao Sun and Zuhong Lu",

note = "Funding Information: This research is funded by the National Grand Fundamental Research Project No. G1998051200 and the National Natural Science Foundation No. 69525102.",

year = "2002",

doi = "10.1016/S0303-2647(02)00016-3",

language = "English (US)",

volume = "65",

pages = "199--207",

journal = "BioSystems",

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T1 - Cluster analysis of the codon use frequency of MHC genes from different species

AU - Ma, Jianmin

AU - Zhou, Tong

AU - Gu, Wanjun

AU - Sun, Xiao

AU - Lu, Zuhong

N1 - Funding Information: This research is funded by the National Grand Fundamental Research Project No. G1998051200 and the National Natural Science Foundation No. 69525102.

PY - 2002

Y1 - 2002

N2 - The relative synonymous codon use frequency of 135 MHC genes from four mammal species (Homo sapiens, Pan troglodyte, Macaca mulanta and Rattus norvegicus) is analyzed using a hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions. The conclusion may be useful in gene classification and gene function prediction.

AB - The relative synonymous codon use frequency of 135 MHC genes from four mammal species (Homo sapiens, Pan troglodyte, Macaca mulanta and Rattus norvegicus) is analyzed using a hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions. The conclusion may be useful in gene classification and gene function prediction.

KW - Codon usage bias

KW - Hierarchical cluster analysis

KW - MHC

KW - Relative synonymous codon use frequency (RSCU)

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EP - 207

JO - BioSystems

JF - BioSystems

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ER -

Cluster analysis of the codon use frequency of MHC genes from different species

Abstract

Keywords

ASJC Scopus subject areas

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