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Expansion method for DNA methylation chip data

An extension method, a methylation technology, is applied in the direction of electrical digital data processing, special data processing applications, instruments, etc., and can solve problems that affect the practicability of algorithms, slow algorithm speed, and underutilization of methylation level data, etc., to achieve Excellent forecasting performance, improved forecasting speed, and accurate forecasting results

Inactive Publication Date: 2017-07-25
UNIV OF ELECTRONICS SCI & TECH OF CHINA
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Problems solved by technology

This invention integrates 450K chip data, extracts two types of features from it for model construction and achieves good results, but the invention still has the following deficiencies: 1), because the invention uses 36 sequence features, in the specific operation process Acquiring features based on sequences requires a lot of calculations, and under the condition of limited computing resources, the speed of the algorithm will be too slow, which affects the practicability of the algorithm
2), the invention does not make full use of the existing methylation level data obtained based on WGBS to optimize the prediction results based on mathematical models

Method used

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  • Expansion method for DNA methylation chip data
  • Expansion method for DNA methylation chip data
  • Expansion method for DNA methylation chip data

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Embodiment

[0036] figure 1 It is a flow chart of a DNA methylation chip data expansion method of the present invention.

[0037] In this example, if figure 1 As shown, a method for extending DNA methylation chip data of the present invention comprises the following steps:

[0038] S1. Extract data

[0039] 31 different tissues T were obtained from the methylation public database GEO 1 , T 2 ,...,T 31 Whole-genome sulfite sequencing data and DNA methylation microarray data corresponding to 31 tissues; in addition, another arbitrary tissue T 32 Whole-genome sulfite sequencing data and DNA methylation microarray data.

[0040] S2, data preprocessing

[0041]Determine whether there is a null value in each row of the whole genome bisulfite sequencing data and the DNA methylation chip data, and if there is a null value, delete the corresponding row to obtain the standard whole genome bisulfite sequencing data and DNA methylation chip data. Basic chip data;

[0042] S3, feature extract...

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Abstract

The invention discloses an expansion method for DNA methylation chip data. Expansion of the DNA methylation chip data is realized by predicting a CpG locus not covered by a DNA methylation chip. Specifically, first, features of the CpG locus to be predicted are extracted based on measured data of the DNA methylation chip and sequencing data of other whole-genome sulfite with similar tissue; second, a methylation value measured through a whole-genome sulfite sequencing method of the CpG locus to be predicted is combined to train a Logistic regression model; and last, the trained regression model is used to predict new data.

Description

technical field [0001] The invention belongs to the technical field of extension of DNA methylation detection chip, and more specifically relates to a data extension method of DNA methylation chip. Background technique [0002] DNA methylation is the most studied form of modification in epigenetics, and it is also one of the earliest epigenetic phenomena recognized by humans. Changes in DNA methylation patterns can affect changes in genome transcription patterns during normal cell development and play an important role in the occurrence and development of diseases. [0003] At present, we obtain DNA methylation data mainly through experiments to detect DNA methylation status. Although the measured data of this kind of method is more accurate, the cost of human and financial resources is relatively large. Therefore, it is particularly important and necessary to use computational methods to predict DNA methylation data. [0004] The most commonly used methods for DNA methyl...

Claims

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Application Information

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IPC IPC(8): G06F19/12G06F19/24
Inventor 邹见效许杰凡时财何建徐红兵
Owner UNIV OF ELECTRONICS SCI & TECH OF CHINA
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