The field of interaction analysis offers a robust and versatile approach to the investigation of protein interactions and biological networks. This approach has already been applied to the identification of new protein interactions.
STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
Online tool that provides information on protein-protein interactions
Input
Enter the name of the protein of interest, the protein identifier or sequences. The system will return a network of proteins and their interactions.
Interactions are classified into different categories, such as:
Experiment: Based on direct experimental data;
Prediction: suggested by computational methods;
Co-occurrence: Proteins that appear together in studies.
For each protein, STRING provides complementary information, such as biological function, involvement in metabolic pathways and other relevant data.
Results
Interactions are presented in the form of a network, where proteins are represented by nodes and interactions by edges. The strength of interactions can be represented by different line thicknesses or colors.
Applications
Basic Research: Understanding interactions in biological processes;
Drug Development: identify potential targets for therapeutic interventions;
Genomics: Helps in functional annotation of unknown proteins.
STRING is a biological database of known protein-protein interactions predicted by experimental data. Compiles data from diverse sources, including laboratory experiments, computational predictions, and scientific literature. This allows you to identify known and predicted interactions between proteins.
BioGrid - Biological General Repository for Interaction Datasets
It is a database that organizes information about biological interactions, mainly interactions between proteins and genes. Compiles biological interaction information from diverse sources, including scientific publications, interaction databases, and experiment results.
The database covers different types of interactions, such as:
Protein-protein interactions;
Genetic interactions;
Chemical interactions.
Input
Users can search for specific genes or proteins using names or identifiers.
Filters
You can apply filters to refine results based on interaction types, environments, among others.
Results
A network of interactions is generated, helping to understand how proteins and genes are interconnected.
Applications
Scientific Research: Essential tool for researchers studying molecular interactions in biology.
Genomics: Assists in the functional annotation of genes and proteins.
Drug Development: Facilitates the identification of therapeutic targets.
BioGRID is a database of biological interactions that provides data on physical and genetic interactions, allowing researchers to explore and analyze biological networks, contributing to the understanding of cellular processes and disease mechanisms.
Is an open-source software platform for visualizing and analyzing biological networks, such as interactions between proteins, genes, and metabolites.
How to use
Download Cytoscape from the official website and install it on your computer. Then import your networks or data using the available options.
The user can import data in different formats, such as text files, network files (such as .sif and .csv) and even databases such as BioGRID and STRING. The software provides tools for quantitative network analysis, including centrality, modularity, and community detection metrics.
Results
Creates and enables the visualization of complex networks of interactions, representing entities (such as proteins) as nodes and their interactions as edges.
Cytoscape has a wide range of plugins (or “apps”) that expand its functionality, allowing more specific analyses, such as integration of omics data or visualization of metabolic pathways.
Furthermore, it can interact with other software and databases, facilitating the integration of biological data from different sources.
Applications
Systems Biology: Model and understand complex biological interactions;
Genomics: Assists in the interpretation of omics data and the identification of therapeutic targets;
Drug Development: Used to discover new interactions and relevant metabolic pathways.
Cytoscape allows you to visualize and analyze biological networks, enabling researchers to integrate data from multiple sources, such as protein interactions and gene expressions, facilitating the exploration of complex networks and the identification of patterns and relationships in cellular and molecular biology.