"Seeing the Neighbourhood" — Exploring Your Gene in the Genome Browser

 Every gene lives somewhere. It has neighbours — other genes upstream and downstream, regulatory elements scattered around it, histone marks that signal whether the local chromatin is open or closed. When something unusual is happening with your gene of interest, sometimes the explanation isn't in the gene itself — it's in the surrounding landscape.

R2's integrated Genome Browser is where you go to see that landscape.

Unlike external genome browsers that feel disconnected from your expression data, R2's genome browser is woven directly into the platform. You can arrive there naturally — from a gene expression plot, a differential expression result, a correlation list — and the browser opens up showing you the genomic context of whatever you were just looking at, with your data already loaded.

The visual logic is familiar to anyone who has used a genome browser before: horizontal tracks stacked on top of each other, each one showing a different layer of information at the same chromosomal coordinates. Gene models at the bottom. Expression data from your samples above them. Probe or reporter locations mapped onto the sequence. And if ChIP-seq data is available for your samples, histone modification tracks — H3K27ac marking active enhancers, H3K4me3 marking active promoters — painting a picture of epigenomic activity across the region.

What makes R2's browser particularly useful is the ability to toggle between samples and see how the landscape changes. You might look at your gene locus in a high-expressing tumour versus a low-expressing one and notice that a nearby enhancer region is dramatically more accessible in the former. Or you might spot an alternative transcription start site in a subset of samples that nobody in your lab had been aware of.

The zoom and pan controls let you move from a gene-level view down to individual exons, or zoom out to see the broader chromosomal region and spot neighbouring genes that share regulatory architecture with yours. Discovered a suspicious cluster of upregulated genes in your differential expression analysis? Jump to the genome browser and check whether they're all sitting under the same topologically associating domain — a common sign that they're co-regulated by shared enhancers.

You can save complex viewing configurations as profiles — a particular combination of tracks, zoom level and sample selection that you want to return to repeatedly — and share them with collaborators. The genome browser stops being a tool you visit occasionally and becomes a reference you return to throughout a project.

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.