Overview:
This application is a specialized platform developed for the GSC-3587 project.
It provides comprehensive capabilities for gene expression analysis and high-quality data visualization, mirroring the DESeq2 analysis pipeline (DEseq.R).


Scope of Work:
i. Dimensional Reduction analysis (PCA, UMAP))
ii. Quality control (VST PCA, sample distance, outlier flagging)
iii. Model 1 — Global paired DESeq2 (DSS / HR / Immune cluster contrasts, all samples)
iv. Model 2 — Interaction DESeq2 (Compartment x DSS/HR/Immune cluster)
v. Model 3 — Subset analyses (Epithelium-only, Stroma-only)



Feedback welcome: Alireza Heravi Moussavi at amoussavi@bcgsc.ca

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3D Interactive Space

Scree Plot — Variance Explained

Loadings — Top contributing genes

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VST PCA (DEseq.R section 2a/2b)

Sample-to-Sample Distance (VST)

Flagged Outlier Samples (|z| > 3 SD, DEseq.R section 2d)

Samples below are flagged for review only — they are NOT removed from any downstream DESeq2 model.

Samples Used Per Model

design_A and ModelB_Paired run on the full analysis set (all compartments together). Model3_Epithelium and Model3_Stroma are the only models run on a subset (split by Compartment).

All Comparisons Run (design_A / ModelB_Paired / Model3_Epithelium / Model3_Stroma)

DEG Summary (|log2FC|>1, padj<0.05)

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DEG Results

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Uses the Model / Comparison selected in the DEG Tables tab.

Volcano Plot

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Uses the Model selected in the DEG Tables tab.

Top DEGs log2FC Heatmap

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Uses the Model / Comparison selected in the DEG Tables tab.

GO Enrichment Dotplot

GO Term Table

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Uses the Model / Comparison selected in the DEG Tables tab.

KEGG Pathway Dotplot

KEGG Pathway Table

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Uses the Model / Comparison selected in the DEG Tables tab. Ranked on the DESeq2 Wald statistic.

GSEA Enrichment Plot

GSEA Results Table