7 Protein Interaction

This tool focuses on protein-protein interaction analysis of Eucalyptus. It integrates multi-source evidence (experiments, literature, genomic predictions, etc.) through the STRING database to construct an interaction network between Eucalyptus proteins. This function can help decipher the molecular mechanisms of core physiological processes such as Eucalyptus growth and stress resistance, providing key support for functional gene research and targeted breeding of Eucalyptus.

7.1 Operation Demonstration

7.1.1 Enter Eucalyptus-Specific Protein IDs

In the "Query Proteins" input box, enter Eucalyptus-specific protein IDs separated by spaces or commas. Example query:

EUGRSUZ_C02720 EUGRSUZ_C02894 EUGRSUZ_D02251 EUGRSUZ_F01229 EUGRSUZ_F03074 EUGRSUZ_H02295 EUGRSUZ_H04045 EUGRSUZ_I00055 EUGRSUZ_I00628

Figure 7.1: Screenshot of Eucalyptus-specific protein ID input interface for Protein Interaction

7.1.2 Set Analysis Parameters

Minimum Confidence Score: This parameter is used to filter the reliability of interaction relationships, providing multiple threshold levels:

• Highest (0.900): Retains only extremely high-quality interactions, resulting in the most streamlined network;
• High (0.700): High-confidence interactions, balancing reliability and network scale;
• Medium (0.400): Medium confidence (default selection), suitable for most analysis scenarios;
• Low (0.150): Low confidence, resulting in the most abundant network;
• Custom Value: Custom threshold to meet special analysis needs.

Figure 7.2: Screenshot of Minimum Confidence Score setting interface for Protein Interaction

Figure 7.3: Screenshot of custom Minimum Confidence Score setting interface for Protein Interaction

Network Flavor: Two modes are available for constructing interaction networks:

• Evidence: Integrates multi-source interaction evidence such as experiments, literature, and calculations, suitable for global functional analysis of Eucalyptus proteins;
• Confidence: Constructs the network based on confidence weights, emphasizing the quantitative reliability of Eucalyptus protein interactions.

Figure 7.4: Screenshot of Network Flavor setting interface for Protein Interaction

7.1.3 Generate and Download the Interaction Network

Click the "Generate Network" button to generate a customized Eucalyptus protein interaction network. The platform provides multiple download options for result preservation and academic use:

• Download TSV: Downloads the interaction relationship table, including Eucalyptus protein pairs, confidence scores, and species-specific protein annotations;
• PNG/High-Res PNG: Downloads network visualization images (high-resolution PNG format is suitable for academic presentations and publications);
• SVG: Downloads vector graphics format, supporting unlimited scaling without quality loss.

Figure 7.5: Screenshot of interaction network generation and download interface for Protein Interaction

7.2 Result Analysis

Network Visualization Interpretation

The interaction network uses nodes and edges to represent Eucalyptus protein interactions, with clear visual encoding rules:

Nodes (Colored Circles)

Each node represents a Eucalyptus protein. The color of nodes is strongly associated with Eucalyptus functional modules (e.g., proteins related to secondary metabolism have a unique color system). Nodes with high connectivity (such as EUGRSUZ_F01229) are core regulatory proteins in Eucalyptus, which can be used as key targets for genetic improvement and functional verification.

Edges (Connecting Lines)

Edges represent interaction relationships between Eucalyptus proteins, and their color characteristics are determined by the Network Flavor mode:

• When Network Flavor = Evidence is selected: The network integrates multiple types of evidence, and edges have richer colors (e.g., yellow represents transcriptional co-expression evidence, which is related to the expression pattern of Eucalyptus growth stages), intuitively reflecting the multi-dimensional support of interactions;
• When Network Flavor = Confidence is selected: Edges have a more uniform color, focusing on emphasizing confidence weights, facilitating quick focus on high-reliability interaction relationships in Eucalyptus.

View Protein Details by Clicking Nodes.After generating the interaction network, click any node to instantly display a pop-up window with exclusive information about the Eucalyptus protein, including three core information modules:

Basic Information

Includes Eucalyptus protein ID (e.g., EUGRSUZ_C02720), gene name, and species origin (clearly marked as "Eucalyptus grandis") to ensure the uniqueness and species specificity of the target protein.

Functional Annotation

Provides Eucalyptus-specific functional descriptions (e.g., "participates in lignin monomer synthesis", "drought resistance response regulator") and the affiliated gene family (e.g., cytochrome P450 family), helping to quickly clarify the biological function of the protein.

Associated Information

Covers annotated Eucalyptus secondary metabolic pathways and transcriptomic expression characteristics (e.g., "highly expressed in leaves"), providing context for analyzing the role of proteins in Eucalyptus physiological processes.

Figure 7.6: Screenshot of Eucalyptus protein interaction network result and detail view

Figure 7.7: Screenshot of Eucalyptus protein interaction network node detail pop-up

Link to STRING Official Website for In-Depth Data

A dedicated "STRING" label is displayed on the network interface (located on the side of the network). Click this label to directly jump to the corresponding page of the STRING official database to obtain more comprehensive in-depth data for Eucalyptus protein research:

Details of Interaction Evidence

Views the specific sources supporting Eucalyptus protein interactions, such as raw data from experimental technologies (co-immunoprecipitation, yeast two-hybrid, mass spectrometry, etc.), and relevant literature citations (including authors, journals, and publication years), clarifying the scientific basis of interaction relationships.

Extended Functional Annotation

Obtains more abundant protein information, including Eucalyptus protein amino acid sequences, domain predictions, precise annotations of subcellular localization, and multi-dimensional GO/KEGG annotations integrated by the STRING database (supplementing functional entries not covered by the Eucalyptus-specific database).

Data and Tool Expansion

Supports downloading more detailed interaction data (e.g., raw confidence scores, evidence classification tables) and uses advanced tools built into STRING such as network topology analysis and functional enrichment analysis to further deepen the mechanism research of Eucalyptus protein interactions.

Figure 7.8: Screenshot of STRING official website link entry for Protein Interaction