Clustering method based on network for disease subtype problem

A clustering method and gene regulatory network technology, applied in the field of network-based clustering, can solve the problem of not considering the correlation of gene expression data

Inactive Publication Date: 2015-12-16
杭州奥视图像技术有限公司
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Problems solved by technology

However, in previous studies, people only used traditional clustering methods, and did not consider the correlation between gene expression data.

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  • Clustering method based on network for disease subtype problem
  • Clustering method based on network for disease subtype problem
  • Clustering method based on network for disease subtype problem

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Embodiment Construction

[0055] Below in conjunction with accompanying drawing and specific embodiment the present invention is described in further detail:

[0056] Now, we assume that there are 32 subjects P 1 ,P 2 ,...,P 32 , where subject P 1 ,P 2 ,...,P 8 As a normal patient, subject P 9 ,P 10 ,...,P 16 for genetic disorder subtype D 1 patient, subject P 17 ,P 18 ,...,P 24 have genetic disorder subtype D 2 , subject P 25 ,P 26 ,...,P 32 have genetic disorder subtype D 3 . D. 1 、D 2 、D 3 Each of the subtypes in represents abnormal expression of certain genes. In order to simulate this abnormal expression process, for a certain subtype, we randomly select a certain node (that is, a gene) from the entire gene regulatory network, and its maximum transcription rate m i Make a disturbance. For different subtypes, we select different genes for perturbation. What we hope to do is to try to separate the control group from the three disease subtypes by performing cluster analysis on ...

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Abstract

The present invention relates to the field of reverse research of disease subtype, and aims to provide a clustering method based on a network for disease subtype problems. The clustering method based on the network for disease subtype problems comprises the processes: obtaining an O-G matrix and a gene regulatory network; selecting a distance definition based on the network applicable to specific questions, and constructing a distance matrix; and using a K-medoids algorithm to perform clustering analysis on the O-G matrix, and selecting a distance based on the network for the clustering distance. The method provided by the invention has a better inter-group similarity to a specific gene network, and reduction of three subtypes can be effectively carried out; and when expression data of a large number of genes needs to be determined, the identification effect of disease subtype is not greatly weakened by precisely measuring the expression data of information genes preferentially.

Description

technical field [0001] The present invention relates to the field of reverse research on disease subtypes, in particular to a network-based clustering method for the problem of disease subtypes. Background technique [0002] Research on diseases caused by genetic mutations has always been a very hot topic. Many of these diseases have different subtypes. The so-called subtypes (subtypes) are different types of the same disease. They may have different etiologies and have different clinical manifestations. For example, HIV has types 1 and 2, and tumor subtypes include ovarian cancer, lung cancer, and uterine cancer. [0003] Many studies on disease subtypes are still focused on positive research on its pathology at this stage. And the use of reverse engineering technology (reverseengineering), reverse study of disease subtypes has gradually become a hot topic. "Reverse engineering technology" is a process of studying the subject system. It identifies the various componen...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/24
Inventor 孔德兴方红晟
Owner 杭州奥视图像技术有限公司
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