MA Plot

Visualize differential expression results as log2 fold-change versus mean expression (M vs A). Significantly up- and down-regulated genes are highlighted automatically.

Visualization Parameters

Upload your data and generate the ma plot

Upload Data File

TSV/CSV with baseMean, log2FoldChange and padj columns

Required Files

data.tsv — differential expression results (e.g., DESeq2 output)

Format

Row = one gene
baseMean: mean normalized expression (alias: AveExpr)
log2FoldChange: log2 fold-change between conditions (alias: logFC)
padj (optional): adjusted P value; without it, genes are colored by |logFC| only
Column aliases auto-detected (FDR, qvalue, adj.P.Val, ...)

Example Data

Gene	baseMean	log2FoldChange	padj
Gene0000	31.5	1.265	4.90e-05
Gene0001	6351.2	0.402	6.82e-02
Gene0002	847.2	0.438	4.32e-02
Gene0003	248.1	-3.343	7.99e-10

MA Plot

Upload data and click Generate, or run with example data

Documentation

Input format: a tab- or comma-separated table of differential expression results with baseMean, log2FoldChange and optionally padj. Common aliases (AveExpr, logFC, FDR) are recognized automatically.

Color scheme: red = up-regulated (padj < 0.05 & log2FC > 1), green = down-regulated (padj < 0.05 & log2FC < -1), grey = not significant. Dashed lines mark |log2FC| = 1.

Typical use: visualize the output of the Differential Expression module in the Bulk RNA-seq workflow (Active vs Torpor comparisons).