The Immune Atlas¶
Open the atlas → Best on a desktop browser. Drag to orbit, scroll to zoom, click any molecule.
The pathway map explains the four colour-coded streams of the working disease model as a flowchart. This is the same model as a cell you can fly around inside: 217 molecules and 380 interactions across eleven compartments, from the nucleus and the mitochondrion down to a neighbouring lymphocyte.
The embedded view above is fully interactive, but the atlas is designed for a full window — use the button for the real thing.
What you can do with it¶
Enter a compartment. Double-click the mitochondrion and the camera flies inside, revealing detail that stays hidden at the whole-cell level: the VDAC1 macropore, the PNC1/PNC2 nucleotide carriers on the inner membrane, POLG at the mtDNA nucleoid, the respiratory complexes, and the mitophagy machinery that gets flagged and then jammed.
Isolate one arm. Turn every pathway layer off, then turn a single one back on. cGAS–STING alone is legible in a way it never is in a diagram with everything drawn at once.
Trace the coloured streams. The PURPLE, BLUE, RED, GOLD, ORANGE, TEAL and GREEN streams are the ones from The Mitochondrion Under Siege, carrying their original names and attack-vector numbers, so the atlas and the figure can be read side by side. Click one and it lights its whole chain, marking what feeds it and what it hands on.
Step through a cascade. This is the part that is hard to do on paper. Ask for every way the variant induces type-I interferon and the atlas enumerates the routes through the graph — 379 of them, within sixteen steps — then walks you along one reaction at a time, forwards and backwards, with the mechanism and its citation at each step.
Each route carries three things worth knowing:
- Net effect, the product of the polarities along it.
A565T ⊣ SAMHD1 ⊣ NF-κBis a double negative: losing a brake on a brake raises NF-κB. Some routes come out negative, and those are real negative feedback — the ones through IκBα, USP18 and A20 genuinely suppress their endpoint. - Evidence grade, taken from the weakest link on the route, because a chain is only as defensible as its softest step.
- Which feedback loops it passes through.
How confident is any of this?¶
Every molecule and every arrow carries an evidence grade, and the atlas will filter to show you only what survives at each level:
| meaning | |
|---|---|
| S | demonstrated in SAMHD1-deficient cells, animals, or AGS patients |
| G | well established in another immune or mitochondrial system, imported here |
| I | mechanistically consistent extrapolation, not yet tested in SAMHD1 models |
This is the same key used throughout the project's working documents. It is there to be used: set the evidence filter to S only and most of the picture disappears. What remains is the part that can be argued from directly. The rest is a hypothesis with its reasoning shown, which is the honest way to present a model that has not been tested yet.
What it is not¶
It is a qualitative map, not a simulation. An arrow means "acts on", not "acts on with magnitude x". There are no rate constants, no stoichiometry and no time axis, so it can tell you that a route exists and which direction it pushes — but not how much, or how fast, or which route dominates in a real cell.
It is also a model of one variant's predicted biology, assembled from published mechanism. Nothing in it is a clinical finding, and nothing in it is medical advice.
Colophon¶
Built with three.js. No tracking, no analytics, no external requests — the page loads its own code and nothing else. Source and the full citation registry are in the project repository.