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Method for constructing novel visual dynamic protein network reflecting proteome changes

A protein network and proteome technology, applied in special data processing applications, instruments, electrical digital data processing, etc., to achieve the effect of great application value

Active Publication Date: 2013-03-13
BEIJING NORMAL UNIVERSITY
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  • Method for constructing novel visual dynamic protein network reflecting proteome changes
  • Method for constructing novel visual dynamic protein network reflecting proteome changes
  • Method for constructing novel visual dynamic protein network reflecting proteome changes

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Embodiment

[0054] Example, Construction of Protein Regulatory Network Model During Cell G0 / G1 Phase Transition

[0055] 1. Cell culture

[0056] The culture parameters of A549 cells: using RPMI 1640 medium containing 10% calf serum, at 37°C, 5% CO 2 cultured in an incubator. Passage method of A549 cells: Digest the cells with trypsin, then pipette gently several times to disperse the cells. The passaging ratio is 1:3-1:5, and passaging once every 2-4 days.

[0057] Take vigorously growing log phase A549 cells (80% confluence), quickly wash three times with serum-free RPMI 1640 medium, and then culture in fresh serum-free RPMI 1640 medium for 48 hours (5ml / bottle), at this time the cells Enter the G0 phase.

[0058] 1. Pre-experiment

[0059] A549 cells in the G0 phase were transferred to RPMI 1640 medium containing 10% calf serum for culture, and cell samples were taken at 0, 3 and 6 hours of culture, respectively.

[0060] (1) Western blot detection of synchronization effect

[00...

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Abstract

The invention discloses a method for constructing a novel visual dynamic protein network reflecting proteome changes, which comprises the steps of: (1) correcting the expression quantity numerical value of a differential protein in a dynamic proteomic research at each time point: S=(Vtest-Vcontrol) / Vcontrol; (2) uploading an inlet number of a protein database and an S numerical value to a MetaCore network analyzing server and drawing an original protein network map; (3) adjusting the positions of nodes superposed in the original protein network map; (4) activating n data documents sequentially to obtain n network maps with protein expression information at time points, respectively; (5) organizing the network maps in form of flash documents through a time shaft to form a dynamic network map; and (6) adding a cell contour and a popup information frame to the dynamic network map. The method has a significant application value to displaying and researching proteome changes in various biological processes.

Description

technical field [0001] The invention relates to a method for constructing a new type of visible dynamic protein network reflecting the change of the proteome. Background technique [0002] Protein is the direct and main bearer of life activities. Proteins perform and regulate various biological functions through active and complex interactions. With the rapid development of proteomics and bioinformatics, the network has become an important and effective expression form of omics research results, as well as a powerful tool to promote research. Through the efforts of Gandhi et al., the number of interactions between human proteins included in the HPRD database (www.hprd.org) has reached as many as 38,000. Researchers have been looking for a tool that can represent the complex organization of various components (genes and proteins) in cells, and found that protein molecules are represented by vertices or nodes, and the connections or arrows between nodes represent the relatio...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/12
Inventor 何大澄何进军王静郝帅
Owner BEIJING NORMAL UNIVERSITY
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