Method for constructing Eriocheir sinensis protein interaction network

A Chinese mitten crab and protein interaction technology is applied in the field of building protein interaction networks, which can solve the problems of huge differences in protein interaction networks, and achieve the effects of simple and easy operation, high quality and wide sources.

Pending Publication Date: 2022-07-29
TIANJIN NORMAL UNIVERSITY
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Problems solved by technology

However, there are big problems in terms of high-throughput experimental techniques
High-throughput experiments often produce a large number of false positive results, and the protein interaction networks obtained by different methods vary greatly[7,8]

Method used

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  • Method for constructing Eriocheir sinensis protein interaction network
  • Method for constructing Eriocheir sinensis protein interaction network

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[0075] Taking the transcriptome of Chinese mitten crab as the source of gene sequences, and selecting Drosophila, nematode, human, house mouse, brown mouse, and yeast as reference model organisms, a protein interaction network of Chinese mitten crab was constructed. The network contains 8225 proteins and 148524 protein interactions. The specific method is as follows:

[0076] Step 1: Data Collection:

[0077](1) The gene sequence data of Eriocheir sinensis is taken from the transcriptome data of the GEO database. The data includes the transcriptome data of five tissues of Eriocheir sinensis gill, eye stalk, thoracic nerve mass, hepatopancreas, and muscle. Contains 246,232 gene sequences and their functional annotations;

[0078] (2) Obtaining 22,006 Drosophila protein sequences, 26,618 nematode protein sequences, 70,236 human protein sequences, 50,694 house mouse protein sequences, 29,982 brown mouse protein sequences, and 6,721 yeast protein sequences from the Uniprot datab...

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Abstract

The invention discloses a method for constructing a protein interaction network of Eriocheir sinensis, which comprises the following steps of: collecting data: taking organisms in a PINA database as reference mode organisms, obtaining protein sequence information of the reference mode organisms, and respectively obtaining protein interaction information of each reference mode organism from the PINA database and an STRING database; constructing an Eriocheir sinensis protein interaction sub-network based on a reference mode organism; fusing the plurality of Eriocheir sinensis protein interaction sub-networks based on the reference pattern organisms; and expanding the Eriocheir sinensis fusion network to obtain the Eriocheir sinensis protein interaction network. The Eriocheir sinensis protein interaction network constructed by using the method disclosed by the invention is the Eriocheir sinensis protein interaction network with the largest scale and the largest number of protein and protein interaction relationships at present, so that richer information is provided for biological analysis performed by using the network.

Description

technical field [0001] The present invention relates to a method for constructing a protein interaction network. In particular, it relates to a method for constructing the Chinese mitten crab protein interaction network. Background technique [0002] Protein interaction networks are a research hotspot in systems biology. By combining computer models and experimental techniques, analyzing complex biological systems from a systematic perspective can provide guidance and predictions for biological experiments and systems biology research [1]. The protein interaction network reflects the protein-protein interactions in cells. The network not only contains a large amount of signal transduction information, but also contains protein relationships in gene transcription regulation, metabolism, immunity and other aspects. The network has scale-free and small-world properties. After 20 years of development, the genome-scale protein interaction network that has been constructed cover...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/30G16B50/00
CPCG16B20/30G16B50/00
Inventor 郝彤孙金生
Owner TIANJIN NORMAL UNIVERSITY
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