MaGIC Gene Correlation Tool

Welcome to the Gene Correlation & Co-expression Tool by the Molecular and Genomics Informatics Core (MaGIC).

How to Use This Tool

  1. Navigate to the Data Input tab. Upload your expression matrix and optional sample metadata, or click 'Load Demo Data' to explore with a built-in example.
  2. Configure your analysis. Choose a data transformation, optionally subset samples by metadata, and select an analysis mode.
  3. Submit your data. Click the Submit button. The Correlation Analysis tab will become visible once data is loaded.
  4. Run correlation analysis. Use the controls in the sidebar to configure parameters and click 'Run Correlation' or 'Run Correlation Matrix'.
  5. Explore and download. Customize the visualizations, explore the results table, and download plots or data.

Two Analysis Modes

Mode A: Single Gene vs All Genes

Pick one target gene and find its top correlated partners across all samples.

  • Faceted scatter plot grid showing the target gene vs each top correlated gene
  • Regression lines and correlation coefficients per facet
  • Full ranked table of all genes by correlation
  • Single pair viewer for detailed inspection, optionally colored by metadata
Mode B: Gene List Correlation Matrix

Upload or paste a gene set to view the full pairwise correlation matrix as a heatmap.

  • Correlation heatmap with hierarchical clustering
  • Significance markers (*, **, ***) and optional correlation values
  • Support for MSigDB Hallmark and GO gene sets
  • Pairwise correlation table with filtering

Required Input Data

Expression Matrix (required)
  • File format: CSV or TSV
  • Rows: Genes (one gene per row)
  • Columns: Samples (one sample per column)
  • First column: Gene identifiers (symbols or IDs)
  • All remaining columns: Numeric expression values
Gene,   Sample1, Sample2, Sample3
BRCA1,  6.5,     7.1,     5.9
TP53,   8.2,     7.9,     8.5
Sample Metadata (optional)
  • File format: CSV or TSV
  • Rows: Samples (one sample per row)
  • First column: Sample names (must match matrix columns)
  • Additional columns: Metadata variables (used for sample subsetting and scatter plot coloring)
Sample,  Group,    Batch
Sample1, Control,  Batch1
Sample2, Treated,  Batch1
Sample3, Treated,  Batch2

Input Data

Expression Matrix

Sample Metadata (optional)

Use the pre-loaded synthetic expression dataset to explore the tool's features.

Demo dataset: ~3000 genes with co-expression modules across 50 samples in 3 groups.

Correlation Settings
Single Gene vs All
Gene List Correlation Matrix

Download Plot