November 28, 2022

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Tumor protein interaction analysis database

Tumor protein interaction analysis database


Tumor protein interaction analysis database. If you want to directly use the interactive network of this website to make the result graph, this database provides the option of custom adjustment.


For interaction analysis, we have introduced two databases: STRING, BioGRID and ConsensusPathDB. Among them, STRING and ConsensusPathDB are a comprehensive database for querying protein interactions; BioGRID is a database for querying single gene interactions. These comprehensive databases often do not limit the search of diseases. But for different diseases, the mechanism of action within genes is often different. Therefore, traditional interactions are often not necessarily suitable for specific diseases. At this time, high-throughput sequencing data of specific diseases is often needed for further verification. So today I will introduce a database that can interact and verify tumor-related diseases: PINA(https://omics.bjcancer.org/pina/)image

 Tumor protein interaction analysis database 

 

1. Introduction to the background data set

For the interaction between genes, PINA is constructed by integrating the results of multiple data. This database integrates data from interactive databases such as IntAct, BioGRID, MINT, DIP and HPRD.

Tumor protein interaction analysis database

For the subsequent analysis of the interaction in the tumor, TCGA’s RNA-seq and some TCGA+CPTAC protein profile data are used image

For the entire protein network database, it mainly includes two steps, one is to construct a protein interaction database; the other is to further analyze the network.

 Tumor protein interaction analysis database

 

2. Interaction network construction

For the construction of interaction networks, the database provides four methods for constructing networks:

  • 1) Input a protein to find the interaction network related to this gene;
  • 2) Input a series of genes/proteins, and search for this series of genes/ Genes/proteins interacting with proteins;
  • 3) Purposefully query the interaction between two genes/proteins; 4) Find the internal interaction between two sets of genes

For example, we want to find out which proteins interact with these three proteins.

Tumor protein interaction analysis database

The database can enter the gene name and the protein ID of uniprot. Regarding the conversion between the two through biomart

After importing, we can obtain other proteins that interact with these three proteins. The whole result interface consists of two parts,

 

(source:chinanet, reference only)


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