Table 1.
Data collection and statistics in croFGD.
| Database content | Number | Source | Reference |
|---|---|---|---|
| GO terms (genes) | 55,505 (14,527) | Blast2GO tool | Conesa and Gotz, 2008 |
| KEGG pathway (genes) | 213 (5,571) | GhostKOALA tool | Kanehisa et al., 2016 |
| PlantCyc (genes) | 513 (2,421) | Blastp prediction | – |
| Cis-elements (motifs) | 1,035 | Database and literature collection | – |
| Orthologous pairs in Arabidopsis (genes) | 36,882 (14,719) | Blast alignment | – |
| Transcription factor and regulators (members) | 88 (1,702) | iTAK prediction | Zheng et al., 2016 |
| Kinases (members) | 85 (778) | ||
| Carbohydrate-active enzymes (members) | 96 (1,505) | Blast alignment | Lombard et al., 2014 |
| Ubiquitin (members) | 21 (1,192) | Blast alignment | Zhou et al., 2018 |
| Cytochrome P450 (members) | 98 (191) | the cytochrome p450 homepage | Nelson, 2009 |
| Co-expression network nodes (%) | 30,096 (88.9%) | PCC and MR | Aoki et al., 2016 |
| Tissue-preferential network nodes (%) | 29,808 (88.1%) | ||
| Treat-response network nodes (%) | 30,541 (90.3%) | ||
| Protein–protein interaction pairs | 9,377 | InParanoid algorithm | Sonnhammer and Östlund, 2015 |
| miRNA target modules | 143 | psRNAtarget prediction | Dai and Zhao, 2011 |
| Function modules from global network (nodes) | 2,310 (10,757) | CFinder tool | Adamcsek et al., 2006 |
| Function modules from tissue-preferential network (nodes) | 1,849 (12,090) | ||
| Function modules from treat-response network (nodes) | 2,177 (12,073) |