Method for excluding genes irrelevant to biological functions

Abstract

The invention relates to a method for excluding genes irrelevant to biological functions, and belongs to the field of bioinformatics and genome research. Generally, the number of genes of species genomes is tens of thousands, only few target genes are screened, and most of the genes in the genomes are irrelevant to target biological functions, so that exclusion of a part of genes before screening of the target genes is very beneficial to gene screening. The expression quantity of the gene is relatively stable under physiological conditions irrelevant to biological functions of the gene, and when the cell needs the gene to play the biological functions of the gene, the expression quantity of the gene can be obviously changed, so that if the expression quantity of one gene under more than five physiological states relevant to the target biological functions has no obvious difference, the expression quantity of the gene can be obviously changed. If yes, the gene is regarded to be irrelevant to the target biological function. According to the method, biological function-independent genes are excluded from the genome level through a calculation method, and the method has important value for related research of genomes and molecular biology.

Description

Technical Field

[0001] The present invention relates to a method for excluding genes irrelevant to biological functions, and belongs to the fields of bioinformatics and genome research. Background Art

[0002] Screening for genes associated with specific biological functions is one of the important research goals of bioinformatics and genomics. Currently, there are many methods for screening biologically relevant genes, such as gene knockout, overexpression, and genetic markers.

[0003] When cells don't need genes to perform their biological functions, gene expression remains constant. When cells need genes to perform their biological functions, gene expression levels change significantly. However, due to the complexity of cellular metabolism, directly screening for genes related to biological functions based on differential expression will result in the screening of a large number of irrelevant genes. Species genomes typically contain tens of thousands of genes, while target genes generally only a few in number. The vast majority of genes in the genome are unrelated to the target biological function. Because gene expression levels remain relatively stable under physiological conditions unrelated to their biological functions, we can calculate gene expression levels to exclude genes unrelated to the target biological function, thereby providing favorable conditions for gene screening. Summary of the Invention

[0004] 1. Technical Problems to be Solved

[0005] The present invention excludes genes irrelevant to biological functions based on the expression levels of genes under various physiological states, and can provide favorable conditions for screening genes related to specific biological functions.

[0006] 2. Technical Solution

[0007] In order to achieve the above objectives, the main technical solutions adopted by the present invention include:

[0008] (1) Obtain RNAseq data of five or more physiological states related to the biological function of the research target through databases such as GEO and SRA, or directly through high-throughput sequencing technology;

[0009] (2) Calculations were performed using tools such as Hisat2, Tophat, Cufflinks, and Bioconductor to obtain the expression levels of all genes in the species under various physiological states;

[0010] (3) Statistical analysis was performed using tools such as R, SPSS, or EXCEL to calculate the average expression level of each gene under various physiological conditions. If the absolute difference between the expression level of a gene under all physiological conditions and the average value was less than 10% of the average value, the expression level of the gene was considered to have no significant change, and the gene was therefore considered to have no relevance to the target biological function.

[0011] 3. Beneficial Effects

[0012] This method uses RNAseq data to calculate the expression levels of all genes in a species under various physiological conditions and, based on these calculations, excludes genes irrelevant to biological functions. This method has the advantage of eliminating irrelevant genes at a low experimental cost, thus providing favorable conditions for gene screening. This method is of great value to genomic and molecular biology research. DETAILED DESCRIPTION

[0013] In order to better explain the present invention, the present invention is described in detail below by taking the cold stress-related genes of upland cotton as an example.

[0014] (1) Six sets of RNAseq data were obtained from the NCBI SRA database (https: / / www.ncbi.nlm.nih.gov / sra) for upland cotton leaves and roots treated at 4°C for 0 h, 12 h, and 24 h, respectively.

[0015] (2) After quality control and filtering of the RNAseq data, the six groups of RNAseq data were aligned to the upland cotton genome using Hisat2 software, and then the gene expression levels of the six groups of upland cotton RNAseq data were calculated using Cufflinks software. In this example, the gene expression levels were expressed in FPKM. Table 1 selects the expression data of some upland cotton genes for illustration;

[0016] (3) The R language was used to calculate the average expression level of each gene in upland cotton at three time points in two tissues, as well as the significance of the expression difference of each gene under each physiological state. The specific calculation method is as follows:

[0017] (|expression level at a specific tissue and specific treatment time point - average expression level|) / average expression level

[0018] (4) It can be considered that genes whose expression differences are all less than 0.1 under all physiological conditions are genes unrelated to cold stress. Excluding these genes can reduce the workload of screening cold stress-related genes.

[0019] Table 1. Upland cotton gene expression data

[0020]

Claims

1. A method for excluding genes irrelevant to biological functions, characterized in that: It includes the following steps: S1. Obtain RNAseq data of more than 5 physiological states related to the target biological function, and calculate the expression levels of all genes contained in the species genome under these physiological states; S2. Calculate the average expression level of each gene under different physiological states. If the absolute value of the difference between the expression level of a gene under a specific physiological state and the average value is less than 10% of the average value, it is considered that the expression level of the gene under this physiological state has no significant change. S3. If the expression level of a gene does not change significantly under all physiological conditions related to the target biological function, it is considered that the gene is not related to the target biological function.

2. A method for excluding genes irrelevant to biological functions as claimed in claim 1, characterized in that: In step S2, the method for measuring the significance of gene expression differences is: first calculate the average expression level of the gene under all physiological conditions related to the target biological function, and then calculate the absolute value of the difference between the expression level of the gene under a specific physiological state and the average value. If this absolute value is less than 10% of the average value, it is considered that the expression level of the gene has not changed significantly.

3. A method for excluding genes irrelevant to biological functions as claimed in claim 1, characterized in that: In step S3, if the expression level of a gene does not change significantly under all physiological conditions, it is considered that the gene is not related to the target biological function.

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