Mathematical Modeling And Algorithm About3-base Periodicity Of P53Tumor-suppressor Gene

Variant of P53make the wild P53gene lose the function of inhibiting the cancer. Understanding of P53is from tumor antigen and oncogene to tumor suppressor gene.More than half of tumor is closely related to P53gene at present.So,it is one of the most popular gene in biological research.In recent years,gene treatment which could become method to effect a radical cure of cancer has become the focus of cancer therapy.Therefore,P53gene as a target for gene therapy is always a hotspot for tumor treatment research.Base on the research methods of P53and3-base periodicity,the main contents are listed as follows:1. To be more specifically, under the Voss numerical mapping, two indicators, the frequency and the signal-to-noise ratio (R), will be combined to discuss the3-base Periodicity of P53Family Genes, as well as using the discrete Fourier transform (DFT). Exons of the DNA Sequence of human beings’P53Family(P53、P63andP73) and house mice’ P53Family will be selected to study the relation between the3-base periodicity and exon’s length, base composition and base distribution. On the premise of3-base periodicity theory, this paper analyses P53genes’codon bias. The result has illustrated that:the3-base Periodicity of short exons (N<100) in P53Family Genes is not obvious, while the3-base Periodicity of longer exons (100≤N<1000) in P53Family Genes is quite obvious. The exons with the character of3-base Periodicity have a higher content in GC、GC3and the GC content has obvious relations with spectrum pick value.It has the highest possibility that the spectral peak of the3-base Periodicity is G or C and the content of GC3is quite high. The R value has a significant relation with Frequency of Optimal Codons(FOP). There is a positive correlation between the spectrum pick value and P53Family Genes’codon bias.2. Under the Z-curve numerical mapping,3-base periodicity of P53CDS and mRNA was analyzed in order to study P53tumor protein further.And the codon bias of P53CDS and mRNA was discussed through analyzing their RSCU and QRSCU value. The result has illustrated that:the CDS of P53has a3-base periodicity,but the mRNA of P53has no3-base periodicity.The P53CDS has a strong bias that the third base is G or C in the codon.What’s more,it is stronger than that of mRNA.It shows that3-base of periodicity is closely related to the codon usage bias of P53genes.The bias level has an effect on3-base of periodicity.And it is a explanation why it has a difference of3-base of periodicity between CDS and mRNA from biology.It is helpful to improve the correct rate of gene recognition.3. Signal-to-noise ratio threshold is a prerequisite when gene recognition algorithm is proposed base on3-base periodicity.In general let R0=2but the gene length and type has an effect on the threshold.Combined with the existing method for determining the threshold,a new method for determining the threshold is put forward with the weigh base on gene length and exon length.What’s more,100human genes,100rodents genes and200mammalian genes are selected to experiment and analyze. Under the mobile window,gene recognition algorithm base on the threshold.The result has illustrated that:the new threshold is more effective than before.And different type gene has different threshold. The gene recognition algorithm has higher accuracy.The innovations are listed as follows:1. More effective model of judgment3-base periodicity is put forward base on two indicators,frequency and signal-to-noise ratio.2. The relation between P53family genes’ characteristics and3-base periodicity is study using the method of k-means clustering and correlation analysis.3. The difference between3-base periodicity of P53protein coding region and that of the corresponding mRNA is analyzed.And the relation between codon usage bias and3-base periodicity is analyzed base on the value of RSCU and QRSCU.4. The new method is put forward with the weigh base on gene length and exon length for determining the threshold.