PaintOmics

PaintOmics paints your omics measurements onto the pathways that explain them. You upload one file per omic layer, it matches your identifiers to KEGG, Reactome, MapMan and OmniPath, tests which pathways your data has moved, and draws the result on the pathway diagrams themselves — every gene, protein, transcript, region and metabolite you measured, coloured by what it did, in every condition at once.

It runs in a browser and needs no account: a job gets its own URL the moment it starts, and you can close the tab and come back to it.

The home page. Load an example fills the form with a published dataset, ready for you to press Run PaintOmics — the fastest way to see the whole tool work.

What you can do with it

Integrate several omics at once	Gene expression, proteomics, metabolomics, miRNA-seq and any region-based assay (DNase-seq, ChIP-seq, ATAC-seq, Methyl-seq) in one job, with a combined p-value per pathway.
Work across four pathway databases	KEGG, Reactome, MapMan and the OmniPath interaction network, in whatever combination is installed for your species.
See the whole time course on one diagram	Each matched feature is drawn as one box per condition, so a trend is visible without leaving the map.
Go beyond enrichment	A pathway interaction network, a metabolite hub analysis, a metabolite class activity test and regulatory modelling with MORE.
Let the AI agent walk the result	It walks the KEGG, Reactome and OmniPath interactions with your values on them, and writes what the walk shows as a Results section whose every value, leg and citation is checked. See What the AI does.

Start here

• Your first analysis — the whole tool, screen by screen, on a real dataset. Start here if you have never used PaintOmics.
• Preparing your data — what a values file and a relevant-features file look like, for each kind of omic.
• The example datasets — twelve ready-made jobs, from a single gene-expression contrast to the full five-omic STATegra time course.
• A worked example — one real five-omic run followed from the files to a conclusion, and what that conclusion does not support.

The three databases, and the fourth

KEGG is always installed. Reactome, MapMan and OmniPath are installed per species, and the upload form ticks the ones your organism actually has — so what you see offered is what this server can run. If your species is missing entirely, Request an organism on the upload form sends the maintainers a request; any organism KEGG carries can be installed.

Getting help

Report a problem or ask a question at paintomicsai@gmail.com, or open an issue on GitHub. If you use PaintOmics in published work, the More ▸ Cite PaintOmics menu in the application gives the BibTeX for each release.