Hi-C Contact Maps and TAD Triangles
A Hi-C map turns 3D genome folding into a heatmap of contact frequency along a chromosome.
Site connection
The HiC-TAD project visualizes chromatin contacts, TAD architecture, boundaries, polymer models, and deletion effects.
Visual model
Contact intensity around a movable boundary
Shift the boundary and watch contact intensity reorganize into two domains.
Interactive
TAD boundaries appear where contact intensity changes
What the Matrix Means
A Hi-C contact map is a square matrix. Each row and column represents a genomic bin, and each cell records how often two bins were observed near each other in 3D space.
The diagonal is strong because nearby genomic positions often contact each other. Off-diagonal blocks reveal longer-range folding structure.
Why TADs Look Like Triangles
A topologically associating domain is a region whose internal loci interact more frequently with each other than with neighboring regions.
When plotted as an upper triangle, the high-contact square block becomes a triangle. Boundaries show up where the triangle pattern changes.
| Visual feature | Biological interpretation |
|---|---|
| Bright diagonal | Nearby genomic bins contact often |
| Bright block | A domain with enriched internal contacts |
| Boundary line | A transition between interaction neighborhoods |
| Changed block after deletion | Possible structural disruption |
Connection to Deletion Analysis
The project uses wild-type and deletion predictions to ask whether removing a boundary or enhancer-like sequence changes the contact map.
That makes the heatmap more than a visualization: it becomes a structural hypothesis about gene regulation.
Common Pitfalls
- Reading every bright cell as a direct physical contact between two fixed points.
- Ignoring resolution; a 5 kb map and a 100 kb map reveal different structures.
- Comparing heatmaps without normalization.
- Treating TAD boundaries as perfectly sharp walls.
Quick check
Quiz
What does a bright off-diagonal block usually suggest?
- No contacts exist
- Bins in that region contact more often than expected
- The chromosome is deleted
- The bins are always adjacent in sequence
Brightness represents contact enrichment between two genomic regions or within a domain.