Table 1.
Summary of the data sources
| Category | Description | Source/method | Details |
|---|---|---|---|
| Genome | version 2.1 | Phytozome v10 | 33032 |
| version 1.4 | Phytozome v9 | 27608 | |
| version 1 | plantsDB | 34567 | |
| Organelle | NCBI | 194 | |
| miRNA | miRBase, PMRD | 242 | |
| Sequence element | SNP | SorGSB | ∼62 million |
| Repeat masker | Phytozome v10 | 639245 | |
| EST | Phytozome v10 | ∼404650 | |
| Motif | plantCARE, PLACE, AthMap | 930 | |
| Transcriptome | RNA-seq | NCBI/GEO | GSE50464, GSE54709, SRP008469 |
| Microarray | NCBI/GEO | GSE49879 | |
| Interaction | protein–protein interaction | Biogrid, iMEX, Intact TAIR, CCSB, ETRAIN | 3871 genes, 11621 pairs |
| co-expression interaction | PCC,MR | 144,901 positive pairs | |
| 136,596 negative pairs | |||
| miRNA-targets | psRNAtarget | 4,376 pairs | |
| Functional annotation | KEGG pathway | KEGG | 4399 genes, 131 pathways |
| plantCyc pathway | plantCyc | 3377 genes, 535 pathways | |
| KOG | Phytozome v10 | 3150 | |
| Panther | Panther | 2836 | |
| Uniprot | UniProt | 32796 | |
| GO | Phytozome v10, Gramene | 1177 | |
| Domain | Pfam | 3832 | |
| Ortholog | Arabidopsis | 111,461 pairs | |
| rice | 21,176 pairs | ||
| maize | 19,691 pairs | ||
| Gene family | Transcription regulators/factors | plantTFDB, plnTFDB | 2541genes,85 families |
| Carbohydrate-active enzymes | CAZy | 1166 genes, 6 classes, 99 families | |
| Protein kinases | PCC database, iTAK | 1253genes,84 families | |
| Ubiquitins | UUCD | 1846 genes,35 families | |
| Cytochrome P450 | Nelson.et al. | 176 genes, 81 families | |
| Monolignol biosynthesis enzymes | Shakoor et al. | 36 genes,10 families | |
| R-genes | Mace et al. | 231 genes,12 classes | |
| Organelle-genes | NCBI | 194 elements, 2 families |