用图论方法研究核酸序列的密码子使用与基因表达水平的关系

Study on the Relation Between Codon Usage of Nucleic Acids Sequence and Gene Expression Level by Graph Theory Method

研究了Escherichiacoli（115个基因）和SacharomycesYeast（97个基因）核酸序列的密码子使用频率与基因表达水平的关系．将同义密码子按使用频率统计值分成三种特性的密码子：最适密码子（H）、非最适密码子（L）和稀有密码子（R），对每一基因序列的编码区，算出它们各自出现的概率P（H），P（L）和P（R）．以P（H）和P（R）为指标，用图论法聚类，发现每种生物的高低表达基因明显分开，基因表达水平被分为四级：甚高表达基因（VH）、高表达基因（H）、较低表达基因（LM）和低表达基因（LL）．每类基因的表达水平与实验结果保持了很好的相关性，与E．coli和Yeast的现有资料相比，符合很好．

The relations between codon usage and gene expression level for E.coli(115genes) and Yeast(97 genes) were discussed.According to the frequency of synonymous codons in a particular class of genes,the codons were classified into three groups optimal codon (H),nonoptimal codon (L) and rare codon ( R ).For each protein-coding sequence,the probabilities of the three groups of codons,P(H),P(L) and P(R),were calculated.Then according to P(H) and P( R ),genes were classfied by graph Theory method.It was found that genes for each species can be class-ified into four dstinct groups:very high-expressed genes (VH),high-expressed genes (H),moderate-expressed genes (LM) and low-expressed genes (LL).The results were consistent with experimental data and other method.