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Method for identifying cancer biomarkers

A biomarker and cancer technology, applied in the field of cancer biomarker identification, can solve the problems of poor promotion performance and achieve the effect of reducing bias and good promotion performance

Active Publication Date: 2017-08-08
UNIV OF ELECTRONIC SCI & TECH OF CHINA
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Problems solved by technology

Due to the high-dimensional and small sample characteristics of the above data, there may be many combinations of features with the best classification performance obtained by the feature selection method, which also makes the potential biomarkers obtained based on data samples from different sources quite different, and Promotion performance is not good

Method used

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  • Method for identifying cancer biomarkers
  • Method for identifying cancer biomarkers
  • Method for identifying cancer biomarkers

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Embodiment

[0031] figure 1 It is a flowchart of a method for identifying cancer biomarkers in the present invention.

[0032] In this example, if figure 1 As shown, a method for identifying cancer biomarkers of the present invention comprises the following steps:

[0033] S1. Obtain the gene expression data and DNA methylation data of any cancer, as well as the known important genes corresponding to the cancer;

[0034] In this embodiment, the thyroid cancer THCA (thyroid carcinoma) is obtained from the cancer genome public database TCGA as an example to illustrate, and the corresponding DNA methylation data of the 450K chip, as well as the important THCA-related data reported in the literature Gene. Among them, the gene expression data of thyroid cancer THCA has 572 samples and 20503 gene features. The DNA methylation data of the 450K chip has 484 samples and 401833 site features.

[0035] S2, assuming that the gene expression data is a matrix of n×p, n is the number of rows of the...

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Abstract

The invention discloses a method for identifying cancer biomarkers. Genetic expression data and DNA methylation data of cancer are acquired from a public database; the genetic expression data are subjected to pre-processing and feature extraction, and feature genes are obtained; the DNA methylation data are subjected to extension and t-test hypothesis testing, and a differential methylation locus is obtained; finally, comparison with existing genes is performed by means of the differential methylation locus, the intersection of successfully compared existing genes and the feature genes is solved, overlapping genes are obtained and the overlapping genes are identified potential cancer biomarkers.

Description

technical field [0001] The invention belongs to the technical field of gene identification, and more specifically relates to a method for identifying cancer biomarkers. Background technique [0002] A biomarker is a sign of a normal or abnormal state of a disease, and a cancer biomarker is a sign for detecting individuals suspected of having cancer or at risk of developing cancer, and has a guiding role in the diagnosis and treatment of cancer. [0003] Common methods for identifying cancer biomarkers are mainly based on single-source data, such as gene expression microarray data, or DNA methylation data, and simple fusion of multiple data. Due to the high-dimensional and small sample characteristics of the above data, there may be many combinations of features with the best classification performance obtained by the feature selection method, which also makes the potential biomarkers obtained based on data samples from different sources quite different, and The promotion pe...

Claims

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Application Information

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IPC IPC(8): G06F19/24C12Q1/68
CPCC12Q1/6886C12Q2600/154G16B40/00
Inventor 凡时财黄康邹见效何建徐红兵
Owner UNIV OF ELECTRONIC SCI & TECH OF CHINA
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