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Novel algorithm for building cellular metabolism network

A technology of metabolic network and cell metabolism, applied in computing, bioinformatics, special data processing applications, etc., can solve problems such as software development lag, and achieve comprehensive and intuitive results with more results.

Inactive Publication Date: 2013-07-03
SHANGHAI CLUSTER BIOTECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, the current software development is relatively lagging behind

Method used

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  • Novel algorithm for building cellular metabolism network
  • Novel algorithm for building cellular metabolism network

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Embodiment Construction

[0022] The present invention will be further described below in conjunction with the accompanying drawings. refer to Figure 1 ~ Figure 2 , this method includes the following steps:

[0023] Step 1: Obtain metabolomics experimental data;

[0024] Step 2: Select differentially expressed metabolites according to the screening criteria;

[0025] Step 3: Metabolic pathway analysis of metabolites;

[0026] Step 4: Separating the relationship between metabolites in each metabolic pathway;

[0027] Step 5: Build a metabolic network;

[0028] Step 6: Use cytoscape software to generate the final network result.

[0029] Let’s take a known liver cancer metabolomics dataset as an example. The specific implementation steps are as follows:

[0030] Step 1: Download the metabolomics experiment data (URL: www.metabolomicssociety.org / database). The data were collated to form a list of metabolites. Step 2: Perform t-test on the data obtained in Step 1, screen metabolites with p<0.01, ...

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Abstract

The invention discloses a novel algorithm for building a cellular metabolism net. In the invention, according to a known metabolic pathway, a complete metabolic network is produced through integration. The metabolite relation can be observed globally, so as to play a guiding significance to mutual action of a metabolic pathway. In the invention, the following steps are included: step 1: obtaining experiment data of metabonomics; 2: selecting metabolites with differential expression; 3, metabolic pathway analysis is performed on metabolin; step 4: separating the relations of metabolins in each metabolic pathway; step 5: building a metabolic network: and step 6: using cytoscape software to generate a final network result.

Description

technical field [0001] The invention belongs to the field of biotechnology and relates to the research aspect of metabolomics. Background technique [0002] The invention is a new algorithm for constructing a cell metabolite network. It is suitable for biomedical research or basic biological research related to metabolomics. [0003] Metabolomics is the quantitative analysis of all metabolites in organisms following the research ideas of genomics and proteomics. Most of its research objects are small molecular substances with a relative molecular mass of less than 1000. As an important part of systems biology, metabolome has broad application prospects in the field of clinical medicine. Metabolites are the end products of gene expression and are produced under the action of metabolic enzymes. Through the in-depth study of the metabolites of the body, researchers can judge whether the body is in a normal state, but the research on genes and proteins cannot draw such a con...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/26G16B45/00
Inventor 刘极龙
Owner SHANGHAI CLUSTER BIOTECH
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