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[+] AraNet: Full integrated network
[+] Gold Standard: Positive functional gene associations
[+] Sub-networks: Individual networks derived directly from A. thaliana data
| Network | Description | Links |
|---|
| AT-CC | PubMed Central full-text Co-citation links of A. thaliana | 78,000 |
| AT-CX | Co-expression patterns of A. thaliana genes | 500,595 |
| AT-DC | Domain Co-occurrence pattern of A. thaliana genes | 25,000 |
| AT-GN | Gene Neighborhood, Proximity between two Arabidopsis gene orthologs in Prokaryotic genomes | 51,000 |
| AT-HT | High-throughput PPI data of A. thaliana | 8,000 |
| AT-LC | Literature curated PPI of A. thaliana | 5,168 |
| AT-PG | Phylogenetic profiling, Co-inheritance patterns of Arabidopsis ortholog genes across organisms | 66,000 |
[+] Sub-networks: Individual networks derived from networks of other organisms' (Associalogs)
| Network | Description (Association between A. thaliana orthologs) | Links |
|---|
| CE-CC | Co-citation links in C. elegans network (WormNet) | 64,214 |
| CE-CX | Co-expression links in C. elegans network (WormNet) | 63,000 |
| DM-CX | Co-expression links in D. melanogaster network(FlyNet) | 96,000 |
| DR-CX | Co-expression links in D. rerio network (DanioNet) | 46,000 |
| HS-CX | Co-expression links in H. sapiens network (HumanNet) | 120,000 |
| HS-HT | High-throughput PPI in H. sapiens network (HumanNet) | 46,000 |
| HS-LC | Literature curated PPI in H. sapiens network (HumanNet) | 87,000 |
| SC-CC | Co-citation links in S. cerevisiae network (YeastNet) | 96,152 |
| SC-CX | Co-expression links in S. cerevisiae network (YeastNet) | 71,000 |
| SC-GT | Genetic interactions in S. cerevisiae network (YeastNet) | 19,000 |
| SC-HT | High-throughput PPI in S. cerevisiae network (YeastNet) | 57,000 |
| SC-LC | Literature curated PPI in S. cerevisiae network (YeastNet) | 89,866 |
[+] Ortholog relationships: A. thaliana and 27 plant orthologs by BLAST Bi-directional Best Hits
| Organism | Number of orthologs |
|---|
| Brachypodium distachyon | 10,904 |
| Brassica rapa | 19,147 |
| Carica papaya | 11,791 |
| Cicer arietinum | 11,934 |
| Citrus sinensis | 12,396 |
| Elaeis guineensis | 9,139 |
| Fragaria vesca | 11,465 |
| Glycine max | 13,809 |
| Gossypium raimondii | 13,650 |
| Malus domestica | 12,436 |
| Medicago truncatula | 9,994 |
| Musa acuminata | 10,986 |
| Oryza sativa subsp. japonica | 10,844 |
| Phaseolus vulgaris | 12,782 |
| Populus trichocarpa | 13,642 |
| Prunus mume | 12,500 |
| Prunus persica | 12,670 |
| Selaginella moellendorffii | 7,089 |
| Setaria viridis | 11,906 |
| Solanum lycopersicum | 12,397 |
| Solanum tuberosum | 11,225 |
| Sorghum bicolor | 10,875 |
| Thellungiella halophila | 19,691 |
| Theobroma cacao | 13,179 |
| Triticum aestivum | 12,586 |
| Vitis vinifera | 11,398 |
| Zea mays cv. B73 | 10,899 |
| Spirodela polyrhiza | 10,316 |
