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🌋 Differential Expression & Volcano Studio

The Differential Expression & Volcano Studio (Tab 9) provides an interactive, publication-ready environment for pairwise and group-level statistical comparisons across cell types, patient cohorts, or experimental conditions.

🎯 Key Capabilities

  • Bidirectional Wilcoxon Rank-Sum Testing: Rapid computation of Log2(Fold Change) and Benjamini-Hochberg FDR-adjusted $p$-values across thousands of genes.
  • Multi-Term Union (OR) Gene Search: Real-time filtering and visualization of gene families or target marker lists (e.g. ITGB, LAM, COL or ITGB.LAM.COL).
  • Interactive SVG Volcano Studio: High-precision interactive volcano plot with dynamic significance thresholds, pure SVG z-ordering, and smart anti-collision gene callouts.
  • Spatially Aligned DEG Tables: Synchronized tables reflecting the volcano plot layout (Downregulated on the Left, Upregulated on the Right) with instant CSV export.

🔍 Multi-Term Union Gene Search & Filtering

Under the Display Controls section, use the search input to filter and highlight specific genes of interest in real time.

Flexible Query Delimiters

The search parser supports multiple delimiter types, enabling quick copy-pasting from gene lists or literature: - Comma-separated: ITGB1, LAMB3, COL17A1 - Dot-separated: ITGB.LAM.COL - Space or semicolon-separated: KRT14 KRT5; ACTB

Union Matching Logic

  • The search evaluates each token independently across both Gene Symbols and Ensembl / Gene IDs (case-insensitive).
  • Results represent the union (OR) of all matches: any gene matching at least one token is selected and displayed.
  • The UI dynamically displays the active search query summary: 
    Highlighting & filtering union of matches for: 'ITGB', 'LAM', 'COL'

🌋 Interactive Volcano Plot Features

The Volcano Plot provides deep insight into global transcriptomic changes with full user interactivity:

1. Dynamic Cutoffs

  • Log2 Fold Change Threshold ($|\log_2\text{FC}|$ cut-off): Adjust via slider to filter for biologically meaningful effect sizes (default: 1.0).
  • FDR Adjusted $p$-value Threshold ($-\log_{10}(p_{\text{adj}})$): Filter for statistical significance (default: 0.05).
  • Visualized as dashed reference threshold lines (red/blue for fold changes, grey for significance).

2. Pure SVG Z-Ordering & Highlight Rings

  • Built with Plotly's explicit SVG rendering mode (render_mode="svg"), ensuring consistent DOM layering across all devices:
  • Background Layer: Non-significant genes rendered in muted grey (#CBD5E1).
  • Significance Layer: Upregulated genes in coral red (#EF4444) and downregulated genes in vibrant blue (#3B82F6).
  • Highlight Layer: Matched genes are enclosed in crisp, hollow purple marker rings (#8B5CF6, 3px stroke width) strictly on the top layer, preserving each gene's true significance color inside the ring.

3. Anti-Collision Labels & Headroom Padding

  • Smart Dynamic Offsetting: Gene label badges and arrows dynamically adjust their angles based on scatter density and axis bounds:
  • Points clustered at ceiling thresholds (e.g. capped at $y = 300$) are staggered upward and outward.
  • Points near the baseline ($y = 0$) are offset upward to prevent axis overlap.
  • Y-Axis Headroom: Automatic padding on the top and bottom of the Y-axis ensures that extreme $p$-value dots and rings are never clipped by chart borders.

📋 Spatially Aligned DEG Result Tables

Beneath the Volcano Plot, the Top Differentially Expressed Genes section features dual mirrored data tables aligned with the volcano plot's spatial orientation:

Column Content Significance Filter
Left Table Top Downregulated Genes in target group Negative $\log_2\text{FC}$, FDR $\le 0.05$
Right Table Top Upregulated Genes in target group Positive $\log_2\text{FC}$, FDR $\le 0.05$

Table Features

  • Real-Time Search Sync: When a search filter is active, tables display only the matching subset (e.g. Matches (18)).
  • Formatted Statistics: Displays Gene Symbol, Gene ID, Log2FC (3 decimals), FDR adjusted $p$-value in clean scientific notation (e.g. < 1e-300, 2.45e-12), and Wilcoxon Z-score.
  • 📥 Download Full Results: One-click button to download the entire unthresholded differential expression result table as a CSV file (DE_<Target>_vs_<Reference>_<GroupCol>.csv).