Enhanced tissue-specific gene interaction networks
Dataset information
This is a collection of gene-gene interaction networks from various human tissues. The networks capture gene interactions that are specific to human tissues and cell lineages ranging from B lymphocyte to skeletal muscle and the whole brain. In each network, nodes represent genes and edges represent tissue-specific functional associations between genes.
| Dataset statistics | |
|---|---|
| Tissues | 22 |
| Nodes | 25825 |
| Edges in tissue central_nervous_system | 162492721 |
| Edges in tissue epidermis | 158818170 |
| Edges in tissue neuron | 243874761 |
| Edges in tissue heart | 121110631 |
| Edges in tissue skeletal_muscle | 123841014 |
| Edges in tissue blood_platelet | 146263529 |
| Edges in tissue chondrocyte | 238930002 |
| Edges in tissue muscle | 142509370 |
| Edges in tissue embryo | 146713307 |
| Edges in tissue smooth_muscle | 179472548 |
| Edges in tissue retina | 168381960 |
| Edges in tissue blood_plasma | 156621439 |
| Edges in tissue blood_vessel | 143976571 |
| Edges in tissue lymphocyte | 141885392 |
| Edges in tissue brain | 162851895 |
| Edges in tissue natural_killer_cell | 208836746 |
| Edges in tissue bone | 158767553 |
| Edges in tissue nervous_system | 162760765 |
| Edges in tissue cardiac_muscle | 208475128 |
| Edges in tissue t_lymphocyte | 144593277 |
| Edges in tissue b_lymphocyte | 144870522 |
| Edges in tissue blood | 176787032 |
The networks are constructed based on raw tissue-specific gene interaction networks, which are normalized and denoised using network enhancement algorithm.
References
- Understanding multicellular function and disease with human tissue-specific networks. Greene, Casey S., et al. Nature Genetics. 2015.
- 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 |
|---|---|---|
| GG-NE.tar.gz | 19GB | Gene-gene interaction networks and statistics (one network per human tissue, nodes are given by NCBI Entrez Gene IDs) |