5 Gene expression

This platform is a specialized tool for querying and visualizing Gene expression data of Eucalyptus across multi-species and multi-scenarios. It integrates transcriptome sequencing data of Eucalyptus (such as Eucalyptus grandis, E. camaldulensis, E. globulus, etc.) under conditions including tissue development and stress responses (cold, boron, salt, nitrogen, etc.). Through multiple visualization methods (bar chart, pie chart, line chart, heatmap, radar chart, polar area chart, etc.), complex gene expression data is converted into intuitive graphs. This helps users quickly explore the expression patterns of Eucalyptus genes in different tissues, developmental stages, and stress conditions. The platform also supports downloading of data tables and SVG vector graphics, meeting the dual needs of scientific research analysis and result presentation, and greatly reducing the technical threshold for Eucalyptus gene function research.

5.1 Operation Demonstration

5.1.1 Select Dataset

In the "Select the query table" dropdown menu, choose the target Eucalyptus dataset. The platform supports multiple Eucalyptus species and experimental types, such as:

eucalyptus_grandis_specific_tissues_development.

Figure 5.1: Screenshot of Eucalyptus dataset selection interface for Gene expression

In the "Select the columns to display" section, check the sample types to be analyzed (e.g., tissues, developmental stages, stress treatment groups). Examples include:

• xylem_6month (xylem of 6-month-old seedlings)
• phloem_3y_plant (phloem of 3-year-old plants)
• flower_3y_plant (flowers of 3-year-old plants)
• lateral_branch_3y_plant (lateral branches of 3-year-old plants)

Figure 5.2: Screenshot of Eucalyptus sample type selection interface for Gene expression

5.1.2 Enter Gene IDs, Select Visualization Charts, and Generate Analysis

In the "Enter Geneid value" input box, enter the target Eucalyptus gene IDs (supports multiple IDs separated by English commas, Chinese commas, or spaces). Example:

LOC104414170 LOC104414171 LOC104414172 LOC104414173 LOC104414174 LOC104414175

In the "Select the type of visualization chart" section, check the required chart types (supports combined selection of bar chart, pie chart, line chart, heatmap chart, radar chart, and polarArea chart). If no chart type is selected, no visualization will be displayed.

Click the "Generate Analysis" button. The platform will automatically generate the gene expression data table and corresponding visualization charts.

Figure 5.3: Screenshot of gene ID input and visualization chart selection interface for Gene expression

5.1.3 Supported Downloads

Data & Chart Download Options

Data Table Download

Click the "Download Table" button to obtain raw Gene expression data in CSV format. The table includes complete expression values of target genes across all selected samples, facilitating further statistical analysis in software such as Excel or R.

Visualization Chart Download

Each generated chart has an "SVG" button in its upper right corner. Clicking this button downloads the chart in high-definition vector graphics format, which supports unlimited scaling without quality loss and is suitable for typesetting in academic papers, research reports, or presentation slides.

5.2 Result Analysis

5.2.1 Raw Data Table of Eucalyptus Gene Expression

The raw expression data table follows a "gene × sample" matrix structure, with core information as follows:

• Rows: Each row corresponds to one Eucalyptus target gene (identified by Gene ID, e.g., LOC104414170).
• Columns: Each column corresponds to one sample type (e.g., xylem_6month, phloem_3y_plant), with clear labels of tissue/organ and developmental stage.
• Values: The numerical values in the table represent the expression activity of genes in the corresponding samples (calculated as FPKM/RPKM). Higher values indicate more active gene expression.

Figure 5.4: Screenshot of Eucalyptus Gene expression raw data table

5.2.2 Interpretation of Visualization Charts

Gene Expression Bar Chart

Core Function

Intuitively compare the expression differences of single or multiple Eucalyptus genes across different samples, enabling quick identification of samples with high/low gene expression.

Chart Interpretation

• Vertical Axis: Represents "expression value" (FPKM/RPKM); higher values indicate more active gene expression.
• Horizontal Axis: Represents "sample types" (e.g., different tissues, developmental stages, or stress treatments).
• Example Insight: For gene LOC104414172, the bar corresponding to "phloem_3y_plant" is the highest, indicating this gene may play a key role in phloem development of 3-year-old Eucalyptus, and its function can be further explored in the context of nutrient transport.

Figure 5.5: Screenshot of Eucalyptus Gene expression bar chart

Gene Distribution Pie Chart

Core Function

Show the proportion of a single Eucalyptus gene’s total expression across all selected samples, helping locate the "predominant expression scenario" of the gene.

Chart Interpretation

• Sector Area: A larger sector area indicates a higher proportion of the gene’s expression in the total expression across all samples.
• Example Insight: The sector of gene LOC104414172 in "phloem_3y_plant" accounts for over 50% of the total expression, confirming this gene is mainly expressed in the phloem of 3-year-old Eucalyptus and is a core candidate gene for phloem function research.

Figure 5.6: Screenshot of Eucalyptus Gene expression pie chart

Expression Trend Line Chart

Core Function

Track the dynamic expression trend of Eucalyptus genes with developmental stages (e.g., 6-month-old → 3-year-old → 6-year-old) or stress treatment duration (e.g., 0h → 6h → 12h → 24h).

Chart Interpretation

• Horizontal Axis: Represents "time/developmental stages" (e.g., xylem_6month → xylem_3y_plant → xylem_6y_plant).
• Vertical Axis: Represents "expression value"; an upward trend indicates increasing gene expression, while a downward trend indicates decreasing expression.
• Example Insight: If a gene’s expression in Eucalyptus xylem shows a continuous upward trend from 6-month-old seedlings to 6-year-old plants, it suggests the gene is involved in the formation and maturation of Eucalyptus wood.

Figure 5.7: Screenshot of Eucalyptus Gene expression trend line chart

Gene Expression Heatmap

Core Function

Batch display the expression "heat" clustering of multiple Eucalyptus genes across multiple samples, enabling rapid screening of "tissue-specific genes" or "stress-responsive genes."

Chart Interpretation

• Color Intensity: Darker colors (e.g., yellow) indicate higher gene expression levels; lighter colors (e.g., purple) indicate lower expression levels.
• Rows: Each row represents one Eucalyptus gene.
• Columns: Each column represents one sample type.
• Example Insight: If a row (gene) shows dark colors consistently across all "cold stress samples" (e.g., cold_6h, cold_12h) but light colors in control samples, this gene is a key candidate for Eucalyptus cold stress response.

Figure 5.8: Screenshot of Eucalyptus Gene expression heatmap

Gene Feature Radar Chart

Core Function

Compare the expression characteristics of multiple Eucalyptus genes from multi-dimensional perspectives (e.g., different tissues, stress treatments) in a single chart, intuitively reflecting functional biases of genes.

Chart Interpretation

• Coordinate Axes: Each axis represents one sample type (e.g., xylem_6month, root_3y_plant, salt_12h).
• Axis Values: The value on each axis represents the gene’s expression level in the corresponding sample; a longer extension from the center indicates higher expression.
• Example Insight: Gene A extends significantly on the "root_3y_plant" and "salt_24h" axes, while Gene B extends more on the "leaf_3y_plant" and "drought_24h" axes. This suggests Gene A is biased toward nutrient absorption and salt stress response, while Gene B is biased toward leaf function and drought resistance.

Figure 5.9: Screenshot of Eucalyptus Gene feature radar chart

Polar Area Chart

Core Function

Display the multi-dimensional distribution characteristics of Eucalyptus gene expression in a "circular proportion" format, highlighting relative differences in expression levels across samples more intuitively than traditional pie charts.

Chart Interpretation

• Ring Width: The width of each circular segment represents the proportion of the gene’s expression in the corresponding sample; a wider ring indicates a higher expression proportion.
• Example Insight: If a gene’s circular segment corresponding to "xylem_6y_plant" is the widest, it indicates this gene has a significant expression advantage in the xylem of 6-year-old mature Eucalyptus, suggesting its potential role in wood formation of mature trees.

Figure 5.10: Screenshot of Eucalyptus Gene expression polar area chart