ReactomeGSA Analysis Report

Report Summary

Reactome Version: -

Date: -

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Pathway Count Summary

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Total
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Significant (p ≤ 0.05)
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Upregulated
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Downregulated

Most Significant Pathways

Top 5 Pathways

Pathway Name FDR

Top 5 Upregulated Pathways

Pathway Name FDR

Top 5 Downregulated Pathways

Pathway Name FDR

Bar Plot

The horizontal bar plot displays the top 20 enriched pathways ranked by statistical significance. Each bar represents a pathway, with the length indicating the -log10 of the adjusted p-value, which reflects the confidence in pathway enrichment. Longer bars imply higher statistical significance.

Bubble Plot

Top 20 significant pathways - Average Log2 Fold Change

This plot shows the the 20 pathways with the lowest adjusted P values, with the Average Log2 Fold Change on the x-axis. The size of each bubble reflects the number of genes associated with the pathway, while the color indicates the direction of regulation: red for upregulated and blue for downregulated pathways.

Bubble Plot

Top 20 Average Log Fold Change pathways (FDR < 0.05)

This plot displays the 20 pathways with the highest changes average expression that also meet the significance threshold (FDR < 0.05). The size of each bubble reflects the number of genes associated with the pathway, while the color indicates the direction of regulation: red for upregulated and blue for downregulated pathways.

Pathway Volcano Plot

The volcano plot visualizes all pathways in terms of their average log2 fold change (log2FC) and statistical significance. The x-axis shows log2FC, indicating the direction and magnitude of regulation, while the y-axis shows -log10 of the adjusted p-value. Each dot represents a pathway:

  • Red: Significantly upregulated pathways (FDR ≤ 0.05 and log2FC > 0)
  • Blue: Significantly downregulated pathways (FDR ≤ 0.05 and log2FC < 0)
  • Gray: Pathways not meeting the significance threshold

Gene Volcano Plot

The volcano plot visualizes all genes in terms of their log2 fold change (log2FC) and statistical significance. The x-axis shows log2FC, indicating the direction and magnitude of regulation, while the y-axis shows -log10 of the adjusted p-value. Each dot represents a gene:

  • Red: Significantly upregulated genes (FDR ≤ 0.05 and log2FC > 1)
  • Blue: Significantly downregulated genes (FDR ≤ 0.05 and log2FC < -1)
  • Gray: Genes not meeting the significance threshold

Pathway Table

Summary of all analyzed pathways along with relevant statistics:

  • Pathway ID: Reactome identifier for the pathway
  • Pathway Name: Descriptive title of the biological process
  • Regulation: Indicates whether the pathway is upregulated or downregulated
  • Adj. p-value: False discovery rate–adjusted p-value representing statistical significance
  • -Log10 (Adj. p-value): Transformed adjusted p-value to highlight significance levels
  • AvgFC: Average log2 fold change of genes within the pathway
  • NGenes: Number of genes associated with the pathway

The table supports interactive exploration: each column can be sorted by clicking the triangle icons next to its header, and columns are resizable by dragging the vertical edge of the header. You can filter the displayed pathways using the checkboxes above the table (e.g., by regulation direction or significance), or search for specific names or values in real-time using the search bar. The table contents can also be downloaded as a CSV file.

Download CSV
Plot Pathway ID ▲ ▼ Pathway Name ▲ ▼ Regulation ▲ ▼ Adj. p-value ▲ ▼ -Log10 (Adj. p-value) ▲ ▼ AvgFC ▲ ▼ NGenes ▲ ▼

Custom Selection Bubble Plot

Select pathways from the table above to compare them in this plot.

No pathways selected. Check the "Plot" box in the table above to add data here.

Gene Expression Table

Summary of gene-level statistics from the differential expression analysis:

  • Identifier: Affymetrix probe set ID
  • Log2FC: Log2-transformed fold change in gene expression between conditions
  • Avg Expr: Average expression level across all samples
  • t-value: t-statistic for differential expression testing
  • p-value: Raw p-value representing statistical significance
  • Adj. p-value: False discovery rate–adjusted p-value to control for multiple testing
  • -Log10 (Adj. p-value): Transformed adjusted p-value to highlight significance levels
  • B-value: Log-odds that the gene is differentially expressed

The table supports interactive exploration: columns can be sorted by clicking the triangle icons in the headers, and you can resize them by dragging the vertical edges. Use the search bar above the table to filter genes by identifier or values in real-time. The table contents can also be downloaded as a CSV file.

Download CSV
Identifier ▲ ▼ Log2FC ▲ ▼ Avg Expr ▲ ▼ t-value ▲ ▼ p-value ▲ ▼ Adj. p-value ▲ ▼ -Log10 (Adj. p-value) ▲ ▼ B-value ▲ ▼