Enhanced Hi-C interaction network
Dataset information
This is a Hi-C interaction network. Hi-C is a chromosome conformation capture (3C)-based technology, an experimental approach for understanding chromatin interactions within DNA. The Hi-C technology measures pairwise chromatin interaction frequencies within a cell population. The genome is divided into bins of equal size (5K bases long), and the number of contacts observed between each pair of bins is reported. Nodes represent genomic regions and weighted edges represent normalized contacts between two regions in the genome.
| Dataset statistics | |
|---|---|
| Nodes (Chromosome 5) | 1419 |
| Edges (Chromosome 5) | 43763 |
| Nodes in largest SCC (Chromosome 5) | 1032 |
| Fraction of nodes in largest SCC (Chromosome 5) | 0.727273 |
| Edges in largest SCC (Chromosome 5) | 32329 |
| Fraction of edges in largest SCC (Chromosome 5) | 0.738729 |
| Average clustering coefficient (Chromosome 5) | 0.867585 |
| Number of triangles (Chromosome 5) | 1235870 |
| Fraction of closed triangles (Chromosome 5) | 0.657262 |
| Diameter (longest shortest path) (Chromosome 5) | 10 |
| 90-percentile effective diameter (Chromosome 5) | 6.561150 |
| Nodes (Chromosome 15) | 1164 |
| Edges (Chromosome 15) | 35470 |
| Nodes in largest SCC (Chromosome 15) | 1054 |
| Fraction of nodes in largest SCC (Chromosome 15) | 0.905498 |
| Edges in largest SCC (Chromosome 15) | 33018 |
| Fraction of edges in largest SCC (Chromosome 15) | 0.930871 |
| Average clustering coefficient (Chromosome 15) | 0.874010 |
| Number of triangles (Chromosome 15) | 999900 |
| Fraction of closed triangles (Chromosome 15) | 0.631299 |
| Diameter (longest shortest path) (Chromosome 15) | 9 |
| 90-percentile effective diameter (Chromosome 15) | 6.088262 |
| Nodes (Chromosome 20) | 720 |
| Edges (Chromosome 20) | 17972 |
| Nodes in largest SCC (Chromosome 20) | 238 |
| Fraction of nodes in largest SCC (Chromosome 20) | 0.330556 |
| Edges in largest SCC (Chromosome 20) | 6760 |
| Fraction of edges in largest SCC (Chromosome 20) | 0.376141 |
| Average clustering coefficient (Chromosome 20) | 0.916722 |
| Number of triangles (Chromosome 20) | 434618 |
| Fraction of closed triangles (Chromosome 20) | 0.649446 |
| Diameter (longest shortest path) (Chromosome 20) | 5 |
| 90-percentile effective diameter (Chromosome 20) | 3.029328 |
The network is constructed based on the raw contact map, which is normalized and denoised using network enhancement algorithm. Shown are network statistics for three human chromosomes, chromosome 5, 15, and 20.
References
- A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Rao, Suhas SP, et al. Cell. 2014.
- Network Enhancement as a general method to denoise weighted biological networks. Bo Wang, Armin Pourshafeie, Marinka Zitnik, Junjie Zhu, Carlos D. Bustamante, Serafim Batzoglou, and Jure Leskovec. Nature Communications. 2018.
Files
| File | Size | Description |
|---|---|---|
| GrGr-NE5K.tar.gz | 3.5MB | Enhanced Hi-C interaction networks and network statistics (one weighted network per human chromosome) |