Method and system for correcting mb-seq methylation level based on ridge regression

A technology of methylation and ridge regression, applied in the field of genetic engineering, can solve problems such as methylation level deviation and achieve the effect of eliminating deviation

Inactive Publication Date: 2018-02-09
DALIAN SANSHENG SCI & TECH DEV
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Problems solved by technology

[0015] Aiming at the problem of the deviation of methylation level existing in the MB-seq—methylated DNA enrichment combined with sulfite flipping methylation detection technology in the prior art

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  • Method and system for correcting mb-seq methylation level based on ridge regression
  • Method and system for correcting mb-seq methylation level based on ridge regression
  • Method and system for correcting mb-seq methylation level based on ridge regression

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Embodiment Construction

[0055] A method for correcting MB-seq methylation levels based on ridge regression, comprising the following steps:

[0056] (1) extracting information (2) modeling (3) ridge regression calculation;

[0057] Wherein, the information to be extracted in step (1) includes: extracting genomic CpG density, GC content and CpG-OE value from the reference genome sequence; The relative methylation information of each cytosine on the genome is known; the absolute methylation information of each cytosine covered is extracted from the unique comparison result of RRBS high-throughput sequencing data;

[0058] The described step (2) is modeled as follows:

[0059]

[0060] in:

[0061] y: objective function; is the absolute methylation information of each cytosine covered by the unique comparison result of RRBS high-throughput sequencing data;

[0062] x: regression variable matrix; including row and column; each row represents each CpG variable; each column is the CpG density, GC con...

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Abstract

The method of correcting MB-seq methylation level based on ridge regression belongs to the field of genetic engineering technology, using machine learning ridge regression theory, and carrying out data training and establishing a prediction model based on the absolute MB-seq methylation level detected by RRBS, for Ridge regression prediction of cytosine sites not covered by RRBS on the genome makes the accuracy of methylation level detection greater than 95%, thereby eliminating the bias of MB-seq and obtaining a genome-wide methylation map. The invention also discloses a methylation level calculation system based on ridge regression. The invention can accurately calculate the methylation level of each CpG in the whole genome from high-throughput sequencing MB-seq data.

Description

technical field [0001] The invention belongs to the technical field of genetic engineering, and in particular relates to a method and system for correcting MB-seq methylation levels based on a mathematical model-ridge regression. Background technique [0002] DNA methylation is one of the earliest discovered modification pathways. A large number of studies have shown that DNA methylation can cause changes in chromatin structure, DNA conformation, DNA stability, and the interaction between DNA and proteins, thereby controlling gene Express. As early as 1942, C.H.Waddinton proposed the concept of epigenetics. He pointed out that epigenetics is opposite to genetics, and mainly studies the relationship between genotype and phenotype. Now, for epigenetics, a more unified understanding is that it studies the reversible and heritable changes in gene function without changes in the DNA sequence of the nucleus. That is to say, on the premise of not changing the genome sequence, gen...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/12
Inventor 张保荣王晓东张久文
Owner DALIAN SANSHENG SCI & TECH DEV
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