Disease and metabolite network construction method based on similarity calculation

A technology of similarity calculation and network construction, applied in biological systems, bioinformatics, informatics, etc., can solve problems such as difficult to analyze disease mechanisms, and achieve the effect of eliminating low efficiency and high cost

Pending Publication Date: 2019-10-18
HARBIN INST OF TECH
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Problems solved by technology

Although complex genes and mirco-RNAs often interact with oth...

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  • Disease and metabolite network construction method based on similarity calculation
  • Disease and metabolite network construction method based on similarity calculation
  • Disease and metabolite network construction method based on similarity calculation

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Embodiment 1

[0041] Embodiment one: if figure 1 As shown, the method for constructing a disease and metabolite network based on similarity calculation involved in this embodiment, the specific steps are:

[0042] Step 1: Obtain information on different diseases and metabolites;

[0043] Step 2: Obtain known metabolites associated with the disease;

[0044] Step 3: Use the InfD-isSim method to find out the similarity of different diseases;

[0045] Step 4: Introduce the MISM method to obtain the similarity of metabolites;

[0046] Step 5: Establish a network of metabolite similarity;

[0047] Step 6: Discover new disease-metabolite relationships by random walk.

Embodiment 2

[0048] Embodiment two: if figure 1 As shown, in the method for constructing a disease and metabolite network based on similarity calculations involved in this embodiment, the acquisition of steps 1 and 2 uses three data sets, which are the human metabolome database, disease ontology and national Biomedical Ontology Center.

[0049] To obtain basic relationships between metabolites and diseases, we use the following three datasets: Human Metabolome Database, National Center for Biomedical Ontology, and Disease Ontology.

[0050] Human Metabolome Database

[0051] We downloaded metabolite data from the Human Metabolome Database (HMDB). The latest and most complete dataset involving more than 40,000 metabolomes. It contains three kinds of data information: chemical data, clinical data and biochemical data. They gathered this information from thousands of public sources.

[0052] The data we get are disease-related metabolites, and they have many complex files. Therefore, we...

Embodiment 3

[0060] Embodiment three: as figure 1 As shown, the method for constructing a disease and metabolite network based on similarity calculation involved in this embodiment, the step three is specifically:

[0061] Each disease has several relevant metabolites, if the number of metabolites is N, the weight vector t1 will be:

[0062]

[0063] is the weight vector of t1, w 1,i is the weight fraction of t1 in the i-th dimension.

[0064] Use cosine to calculate the similarity of diseases, as follows:

[0065]

[0066] Finally, the disease similarity is defined as:

[0067]

[0068] G 1 G 2 Metabolites of t1 and t2 are represented.

[0069] There is some similarity between diseases, and the similarity often arises from molecular origins. The interaction of protein-coding genes can reflect the mechanism of disease to some extent. Therefore, the similarity of diseases can be calculated by the genes behind the diseases.

[0070] To obtain the similarity of diseases, w...

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Abstract

The invention provides a disease and metabolite network construction method based on similarity calculation, and belongs to the field of disease and metabolite similarity network construction. The network construction method comprises the following steps: acquiring information of different diseases and metabolites; obtaining a known metabolite related to the disease; finding out the similarity ofdifferent diseases by using an InfD-isSim method; introducing an MISM method to obtain the similarity of metabolites; establishing a network of metabolite similarity; discovering new disease-metabolite relationship by random walk. By means of the method, more potential metabolites related to diseases can be obtained, and the method has extremely important significance in clinical diagnosis, treatment and development of new targeted drugs; by adopting the method, high cost and low efficiency of biological experiments can be avoided; through the method, the first several candidate metabolites ofa certain disease are determined, and through biological experiment verification, the method is an efficient and money-saving method.

Description

technical field [0001] The invention relates to a disease and metabolite network construction method based on similarity calculation, belonging to the field of disease and metabolite similarity. Background technique [0002] In order to maintain the needs of life, complex and orderly chemical reactions take place in the human body. The whole process is called metabolism. Organisms are dependent on metabolites for their maintenance and growth and reproduction. In terms of how energy is obtained, metabolites are divided into two parts. One is to obtain energy through the catabolism of macromolecules, such as cellular respiration. The other is to obtain energy through cellular synthesis, such as protein and nucleic acid. Once people suffer from diseases, the exchange of matter and energy will be abnormal. A cascade of abnormal metabolites then occurs. Therefore, metabolites can be effective in diagnosing diseases and curing diseases. [0003] Disease understanding at the...

Claims

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Application Information

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IPC IPC(8): G16B5/00
Inventor 胡杨程亮徐培刚赵天意张凝一
Owner HARBIN INST OF TECH
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