8 GO/KEGG enrichment analysis

This tool is a professional gene/protein functional enrichment analysis platform specifically designed for Eucalyptus species, focusing on the biological function annotation of Eucalyptus gene/protein sets. It deeply integrates Eucalyptus-specific KEGG pathway annotation, GO functional annotation, STRING protein-protein interaction network (Eucalyptus species-specific data), and PubMed-related literature association information. From multiple dimensions including metabolic pathways, biological processes, protein interaction neighbors, and literature reports, it rapidly mines the enrichment characteristics of target Eucalyptus gene/protein sets. Applicable to fields such as Eucalyptus molecular breeding, stress resistance mechanism research, lignin synthesis regulation, and essential oil metabolic pathway analysis, it assists researchers in efficiently deducing the potential functions and molecular mechanisms of Eucalyptus genes, providing precise support for Eucalyptus-related omics research.

8.1 Operation Demonstration

8.1.1 Enter Target Eucalyptus Protein IDs

In the left input box labeled "Protein IDs (space/comma separated)", enter the Eucalyptus protein IDs to be analyzed as follows:

example:

EUGRSUZ_H04045 EUGRSUZ_I00055 EUGRSUZ_I00628 EUGRSUZ_J02207 EUGRSUZ_J02208
EUGRSUZ_H04045,EUGRSUZ_I00055,EUGRSUZ_I00628,EUGRSUZ_J02207,EUGRSUZ_J02208

• Enter 1 ID: Automatically expands to 10 Eucalyptus-specific interacting factors;
• Enter ≥2 IDs: Expansion function is disabled, and the target gene set is analyzed directly.

Figure 8.1: Screenshot of Eucalyptus protein ID input interface for GO/KEGG enrichment analysis

8.1.2 Configure Result Parameters

Set the parameters for the enrichment analysis results as follows:

Top N Results:

• Description: Select the number of most significantly enriched terms to return;
• Example: "Top 10" means returning the 10 enriched terms with the smallest FDR among all Eucalyptus categories.

Background (Optional):

• Description: Optionally enter the STRING IDs of the Eucalyptus background gene set (separated by spaces);
• Purpose: Define the Eucalyptus whole-genome background, avoiding enrichment bias caused by mismatched background gene sets and significantly improving the accuracy of Eucalyptus-specific analysis;Note: This field is non-mandatory.

Figure 8.2: Screenshot of result parameter configuration interface for GO/KEGG enrichment analysis

8.1.3 Set Visualization Parameters

Configure the display parameters for the enrichment visualization chart as follows:

Enrichment Category:

• Description: Select the Eucalyptus-specific biological dimension for enrichment analysis;
• Supported categories: KEGG Pathways (Eucalyptus metabolic pathways, e.g., Eucalyptus essential oil synthesis pathway, lignin metabolic pathway), GO Biological Process (Eucalyptus Gene Ontology - Biological Process), GO Molecular Function (Molecular Function), GO Cellular Component (Cellular Component);
• Example: Selecting "KEGG Pathways" focuses on the enrichment analysis of Eucalyptus metabolic pathways.

Figure 8.3: Screenshot of enrichment category selection interface for GO/KEGG enrichment analysis

Color Palette:

• Description: Select the color scheme for visualization charts;
• Example: "Peach Purple", "Mint Blue", etc.;
• Purpose: Distinguish the FDR and gene count of Eucalyptus enrichment results.

Figure 8.4: Screenshot of color palette selection interface for GO/KEGG enrichment analysis

X-Axis Variable:

• Description: Select the quantitative indicator for the X-axis of the enrichment plot;
• Optional options: "Signal", "Strength", "FDR", "Gene Count";
• Example: Selecting "Strength" sorts pathways based on the intensity of Eucalyptus enrichment signals.

Figure 8.5: Screenshot of X-axis variable selection interface for GO/KEGG enrichment analysis

Group Similar Terms:

• Description: Group similar Eucalyptus enriched terms using the Jaccard Index;
• Slider range: 0 ("No Grouping") to 1 ("Strict Grouping");
• Default value: 0.

Figure 8.6: Screenshot of similar terms grouping interface for GO/KEGG enrichment analysis <

8.2 Result Analysis

Enrichment Results Table

The table contains 5 columns of core information, focusing on Eucalyptus-specific interpretation:

CATEGORY

The dimension category of enrichment analysis (e.g., NetworkNeighborAL represents "enrichment of Eucalyptus protein interaction network neighbors"; GO Component, GO Function, and GO Process represent the enrichment of cellular component, molecular function, and biological process in Eucalyptus Gene Ontology, respectively; InterPro represents the enrichment of conserved Eucalyptus protein domains).

TERM ID

The unique identifier of the Eucalyptus enriched term (e.g., CL:9695 for NetworkNeighborAL category, GO:0009326, GO:0008863, GO:0042183 for GO-related categories, and IPR033689 for InterPro category. Eucalyptus-specific annotations can be retrieved in STRING, GO, and InterPro databases using these IDs).

GENES COUNT

The number of target Eucalyptus genes falling under the enriched term (e.g., "6/86" for NetworkNeighborAL category indicates that 6 target Eucalyptus proteins belong to this term, and there are 86 proteins in the Eucalyptus background of this term; "3/3" and "3/4" for GO-related categories reflect the concentration of target Eucalyptus proteins under the corresponding terms).

FDR

False Discovery Rate (FDR of all terms is 0.000000, indicating that these Eucalyptus terms are extremely significantly enriched, and false positives can be eliminated).

DESCRIPTION

Functional description of the Eucalyptus enriched term (e.g., "Citrate cycle (TCA cycle), and Glyoxylate metabolism" for NetworkNeighborAL category; "Formate dehydrogenase complex" for GO Component category; "Formate dehydrogenase (NAD+) activity" for GO Function category; "Formate catabolic process" for GO Process category; "NAD-dependent formate dehydrogenase" for InterPro category).

Enrichment Visualization Figure

A "bubble chart" is used to intuitively display the Eucalyptus KEGG pathway enrichment results. The interpretation of visual elements is as follows:

Color Intensity

Corresponding to FDR value (darker color indicates smaller FDR and higher enrichment significance of the Eucalyptus pathway. For example, the bubble of "Biosynthesis of secondary metabolites" in the figure is the darkest, indicating the smallest FDR and extremely strong enrichment significance).

Bubble Size

Corresponding to GENES COUNT (larger bubble indicates more target Eucalyptus genes falling under the term. For example, the bubble of "Metabolic pathways" in the figure is the largest, indicating that this pathway contains the most target Eucalyptus proteins).

X-axis (Strength)

Represents the intensity of Eucalyptus enrichment signals (calculated as -log10 (FDR); larger values indicate higher enrichment significance of Eucalyptus. The X-axis value of "Citrate cycle (TCA cycle)" in the figure is nearly 2.6, making it the most significantly enriched Eucalyptus pathway).

Y-axis Terms

Eucalyptus enriched terms sorted by the selected X-axis variable (e.g., "Citrate cycle (TCA cycle)" is the rightmost in the figure, with a lighter color and a larger bubble, indicating that this pathway is the core enriched pathway of the target Eucalyptus gene set and is highly correlated with the energy metabolism characteristics of Eucalyptus).

Supported Downloads

Formats: TSV, PNG

Figure 8.7: Screenshot of GO/KEGG enrichment analysis results (table + visualization)