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Dynamic protein complex recognition method

A technology for protein complexes and identification methods, applied in proteomics, biological systems, biostatistics, etc., which can solve the problem that static PPI data cannot provide biological results.

Active Publication Date: 2020-09-15
DALIAN UNIV OF TECH
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Problems solved by technology

Many existing studies are aimed at static PPI data and cannot provide accurate biological results

Method used

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Embodiment approach

[0058] Further as a preferred embodiment of the present invention, the step S1 is specifically:

[0059] S11, the static PPI network is modeled as an undirected graph G=(V, E), wherein V represents a collection of protein nodes, and E represents a collection of edges between protein nodes;

[0060] S12. Determine the activity of the protein based on the gene expression data, and express the gene expression data of N proteins at T time points as an N×T matrix H; at time point t, assume that the gene expression value of a protein i is greater than or is equal to its activation threshold ACT(i), then the protein i is considered active; the expression of its activation threshold ACT(i) is as follows:

[0061] ACT(i)=u(i)+3σ(i)(1-F(i))

[0062] in, represents the average value of protein i from time 1 to T, σ(i) represents the standard deviation of protein i from time 1 to T; F(i)=1 / (1+σ 2 (i)) is a weight equation, which reflects the fluctuation of protein i expression value; ...

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Abstract

The invention provides a dynamic protein complex recognition method. The method comprises the following steps: constructing a dynamic protein interaction network in combination with gene expression data and a static PPI network; clustering the dynamic protein interaction network at each moment based on Markov clustering; optimizing the clustering result through a core attachment structure, and combining the cluster with the core protein and the cluster containing the attachment protein; and filtering highly overlapped protein complexes, and outputting a final protein complex set. The method provided by the invention not only can inhibit the generation of subclasses, but also can identify overlapped proteins. The invention provides a calculation method for identifying the protein complex from a dynamic protein interaction network, which is more in line with the PPI network of the actual biological process and provides a more accurate protein complex identification result.

Description

technical field [0001] The present invention relates to the technical field of bioinformatics, in particular to a dynamic protein complex identification method. Background technique [0002] With the advancement of high-throughput technology, large-scale protein interaction (Protein-ProteinInteraction, PPI) data has been generated. Proteins seldom work alone, they usually combine to form complexes to achieve biological functions. Protein complexes play an important role in understanding the fundamental mechanisms of most cellular functions. Identifying protein complexes from PPI networks helps to predict protein functions and elucidate cellular mechanisms of various diseases. In different phases of the cell cycle, cells have a rapid response mechanism to external stimuli, and the real PPI network changes all the time. Therefore, modeling real PPI networks as dynamic PPI networks can accurately identify more protein complexes. Many existing studies are aimed at static PPI...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B40/30G16B5/30G16B20/00
CPCG16B40/30G16B5/30G16B20/00Y02A90/10
Inventor 梁冰吕嘉庆张益嘉
Owner DALIAN UNIV OF TECH
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