"My Gene, Front and Centre" — Visualising a Single Gene Across Hundreds of Tumours

 It starts, as it so often does, with a hunch.

You've spent months in the lab chasing a gene — let's call it MYCN. You've seen it behave strangely in your cell lines. It seems to go up when it shouldn't, or maybe it's suspiciously quiet in samples where you expected it to roar. The question nagging at you over your morning coffee is: is this pattern real? And does it matter clinically?

The old answer was: ask your bioinformatics colleague, wait two weeks, receive a spreadsheet you can't interpret. The new answer is: open a browser, go to r2.amc.nl, and spend fifteen minutes finding out yourself.

R2's View a Gene module is the front door to the platform, and it's a remarkably welcoming one. You select a dataset — say, a public neuroblastoma cohort with 88 tumour samples — type your gene name into the search box, and within seconds you're looking at a dot plot of expression levels across every single sample. Each dot is a patient. The Y-axis is expression. And already, you're seeing things.

But here's where it gets interesting. R2 lets you colour and sort those dots by clinical "tracks" — annotation layers attached to the dataset, things like tumour stage, age at diagnosis, or MYCN amplification status. Suddenly the scatter of dots reorganises itself into a story. High expressors cluster on one side. Low expressors on the other. And the clinical outcomes? They follow.

You can highlight specific samples, zoom into subgroups, and even ask R2's CliniSnitch feature to automatically find which clinical track best separates your high- and low-expressing samples. It's a little like having a statistician sitting next to you, quietly suggesting: "Have you tried splitting by stage?"

The best part? Everything you see is directly linked back to the underlying data and literature. Click on your gene and R2 surfaces connections to external databases — so you move seamlessly from "interesting expression pattern" to "here's what the world already knows about this gene."

One gene. One afternoon. And you leave with a figure worth discussing at your next lab meeting.

This is Part of an ongoing series on the R2 Genomics Analysis and Visualization Platform, developed at Amsterdam UMC. All analyses can be freely performed at r2.amc.nl. Full tutorials at r2-tutorials.readthedocs.io.