Getting Started
From gene expression data to publication-ready results in three steps.
Upload Your Data
Upload a CSV or TSV file with gene expression data. Column headers become your sample names — we auto-detect groups from naming patterns like WT_rep1, KO_rep2.
Configure & Run
Select which sample groups to compare (e.g., Treatment vs Control). Choose Express for a quick look or Enhanced for the full analysis with pathways and publication plots.
Explore Results
Interactive volcano plots, heatmaps, pathway enrichment, and prioritized gene lists. Download everything as publication-quality figures or filtered data tables.
What File Do I Need?
A CSV or TSV with gene identifiers in the first column and expression values in all other columns. Here's an example:
| gene_id | WT_rep1 | WT_rep2 | KO_rep1 | KO_rep2 |
|---|---|---|---|---|
| BRCA1 | 1542 | 1389 | 423 | 398 |
| TP53 | 8921 | 9102 | 8756 | 8834 |
| MYC | 312 | 287 | 1847 | 1923 |
| GAPDH | 45210 | 44893 | 45102 | 44567 |
Column headers = sample names. The platform groups samples by shared prefixes (WT, KO).
| gene_id | WT_rep1 | WT_rep2 | KO_rep1 | KO_rep2 |
|---|---|---|---|---|
| ENSG00000012048 | 1542 | 1389 | 423 | 398 |
| ENSG00000141510 | 8921 | 9102 | 8756 | 8834 |
| ENSG00000136997 | 312 | 287 | 1847 | 1923 |
Use one format or the other — don't mix gene symbols and Ensembl IDs in the same file.
Accepted
- CSV or TSV files
- Raw counts, TPM, FPKM, or normalized values
- Output from STAR, featureCounts, HTSeq, or similar tools
- Gene symbols (BRCA1) or Ensembl IDs (ENSG00000012048)
- Human or mouse genes (both species supported)
- Any number of samples (2+ per group recommended)
Not Accepted
- FASTQ or raw sequencing files (align first with STAR, Salmon, etc.)
- Matrices not in gene x sample format (e.g., sample x gene)
- Non-human, non-mouse organisms (more species coming soon)
- Pre-computed statistics (fold changes, p-values)
What You'll Get Back
Every analysis produces interactive visualizations and downloadable data.
Volcano Plot
Visualize significant genes by fold change vs statistical significance. Click any point to see gene details.
PCA Plot
See how your samples cluster by overall expression profile. Quickly spot outliers or batch effects.
Heatmap
Top differentially expressed genes across all samples with hierarchical clustering. Publication-ready.
Pathway Analysis
GO biological process and KEGG pathway enrichment. Understand which biological systems are affected.
Gene Prioritization
Prairie's scoring algorithm ranks your genes by druggability, novelty, and statistical confidence. Find actionable targets fast.
Data Tables
Full differential expression results with filtering, sorting, and export. Download as CSV for your own analysis.
Express vs Enhanced
Choose the depth of analysis that fits your needs.
| Feature | Express~30 seconds | Enhanced2-5 minutes |
|---|---|---|
| Differential expression | ||
| Volcano + PCA plots | ||
| Heatmap | -- | |
| Pathway analysis (GO + KEGG) | -- | |
| Gene prioritization scoring | -- | |
| Publication-quality figures | -- |