Table 1.
Coexpression data in ATTED-II version 9
| Species | Platform IDa | Version | Genes | Samples | Logit-MR error | Function scoreb | Reproducibilityc |
|---|---|---|---|---|---|---|---|
| Arabidopsis thaliana | Ath-m | c7.1 | 20,819 | 16,033 | 0.37 | 5.43 | 0.136 |
| Ath-r | c3.0 | 22,760 | 2,120 | 0.71 | 5.17 | ||
| Brassica rapa | Bra-r | c2.1 | 28,978 | 188 | 1.04 | 4.77 | – |
| Glycine max | Gma-m | c3.1 | 15,746 | 1,131 | 0.74 | 3.37 | 0.076 |
| Gma-r | c3.0 | 8,373 | 599 | 1.02 | 7.64 | ||
| Medicago truncatula | Mtr-m | c3.1 | 20,376 | 975 | 1.04 | 4.43 | 0.021 |
| Mtr-r | c1.1 | 3,753 | 41 | 1.46 | 2.65 | ||
| Oryza sativa | Osa-m | c6.1 | 19,867 | 2,250 | 0.76 | 4.98 | 0.041 |
| Osa-r | c2.1 | 24,437 | 336 | 1.07 | 4.06 | ||
| Populus trichocarpa | Ppo-m | c2.1 | 21,910 | 765 | 1.10 | 3.82 | – |
| Solanum lycopersicum | Sly-m | c2.1 | 5,721 | 401 | 1.04 | 4.08 | 0.041 |
| Sly-r | c2.1 | 20,564 | 282 | 1.01 | 3.87 | ||
| Vitis vinifera | Vvi-m | c3.1 | 9,421 | 314 | 1.14 | 4.47 | 0.028 |
| Vvi-r | c1.1 | 18,587 | 346 | 0.90 | 3.10 | ||
| Zea mays | Zma-m | c3.1 | 10,777 | 806 | 1.11 | 4.62 | 0.055 |
| Zma-r | c2.1 | 32,274 | 1,794 | 0.88 | 4.42 |
aXxx-m, microarray-based coexpression; Xxx-r, RNAseq-based coexpression.
bPredictive performance of the KEGG annotation represented by partial AUROC (1E-04). A higher score indicates a better performance.
cJaccard coefficient for common edges between the platforms in the same species. The top three coexpressed genes from every gene were used as edges.