Documentation

OpenPedCanExpress is a browser-based tool for exploring gene expression in pediatric tumors compared with normal tissue controls. Search a gene, compare its expression across tumor histologies and normal samples, and export publication-ready plots.

Quick start

1. Type a gene symbol (for example EGFR, TP53, or CD276) and press Enter.
2. The plot shows expression for each tumor and normal group, with one box per group.
3. Use Configure Groups to choose which cohorts, histologies, molecular subtypes, and normal tissues to show.
4. Optional: customize the export by setting the plot width (Box width), Height, Font size, and file type (PDF, JPG, PNG, or SVG).
5. Use Export Plot to save the figure.

The first load takes a few seconds while the database engine starts. After that, each gene search only downloads the rows for that gene.

Reading the plot

• Facets. Groups are arranged in facets: tumor cohorts first (PBTA, TARGET, GMKF), then normal controls (Pediatric Brain, Evo-devo, GTEx <40). Facet widths are proportional to the number of groups.
• Boxes. Each box spans the first to third quartile with a line at the median. Whiskers extend to the most extreme values within 1.5 × the interquartile range of the box.
• Points. Every sample is drawn as a point, jittered horizontally so overlapping samples stay visible. Hover over a point to see its sample ID and value.
• Y-axis. By default, values are log₂(TPM + 1). Uncheck the log₂ scale option to see raw TPM. The y-axis is shared across all facets so groups can be compared directly.
• Sorting. Tumor groups can be sorted alphabetically or by median expression (high to low, or low to high). Evo-devo groups are always in developmental order.

Configuring sample groups

Open Configure Groups to choose what is plotted.

• Cohorts. All cohorts (PBTA, TARGET, and GMKF) are shown by default, each in its own facet. Uncheck a cohort to hide it.
• Histologies. Tumor groups, listed under their cohort heading.
• Molecular subtypes. Select subtypes to plot those samples separately. Split by molecular subtype divides every tumor group by subtype.
• Control cohorts. Choose GTEx, Evo-devo, and pediatric normal brain groups.

Click Apply to update the plot.

Exporting plots

Choose a format (PDF, JPG, PNG, or SVG; raster images are 300 DPI) and click Export Plot. The export is drawn independently of the on-screen plot, so you can set:

• Box width: pixels per group, which sets the figure width.
• Height of the figure.
• Font size: margins scale with it so labels are not clipped.

The underlying data

Expression values are RSEM TPM, collapsed to gene symbol, from the OpenPedCan project (OpenPedCan v15 data release). All data, tumor and control, was harmonized with the Gabriella Miller Kids First RNA-Seq workflow using the GENCODE v39 reference, so expression values are comparable across cohorts. A preprocessing script (scripts/01-build-expression-parquet.R) converts them into Parquet files split by the first letter of the gene symbol (A–H, I–P, Q–Z). The app queries these files in the browser with DuckDB-WASM, so there is no server or database.

Tumor samples

• RNA-Seq tumor samples from the PBTA, TARGET, and GMKF cohorts.
• Only independent primary specimens are used (one per participant within each cohort), from the OpenPedCan independent specimens list for each cohort.
• PBTA neuroblastoma specimens are excluded.

Normal controls

Control	Description	Data access
GTEx <40	GTEx brain regions, donors aged 20–39	dbGaP phs000424
Pediatric Brain	Non-neoplastic pediatric tissue: Cerebellum, Cortex, Pituitary, Pons	BioProject PRJNA1019377
Evo-devo	Developmental brain from 4 weeks post-conception through elderly	ArrayExpress E-MTAB-6814

The same control cohorts are used in TAPESTRY.

Plot groups

• PBTA. Histology groups come from TAPESTRY, so colors and groups match across Rokita Lab tools.
• TARGET and GMKF. Samples are grouped by OpenPedCan cancer_group. Groups with 3 or fewer samples are not shown, and Ganglioneuroblastoma is combined with Neuroblastoma. The mapping is in plot-groups.tsv.

Glossary

Term	Meaning
TPM	Transcripts per million, a within-sample normalized expression value
log2(TPM + 1)	TPM on a log scale; the +1 keeps zero values defined
PBTA	Pediatric Brain Tumor Atlas cohort
TARGET	Therapeutically Applicable Research to Generate Effective Treatments
GMKF	Gabriella Miller Kids First
GTEx	Genotype-Tissue Expression project (normal tissue)
Independent specimen	One representative specimen per participant, so no participant is counted more than once
Plot group	The category a sample is plotted under (a histology or a normal tissue)

Citing and contact

OpenPedCanExpress is developed by the Rokita Lab. Please also cite OpenPedCan for the underlying data. Questions and bug reports are welcome as GitHub issues.

See the release notes for what changed in each release.