Table 1.
BambooGDB data content and statistics as of 12 October 2013
| Data set | Data type | Data statistics |
|---|---|---|
| Basic data content | DNA/Protein | |
| Genes | 31 987 | |
| Expressed genes (FPKMa ≥ 1) | 28 576 | |
| MicroRNA target genes | 161 | |
| Proteins | 31 987 | |
| RNA | ||
| tRNAs | 1167 | |
| MicroRNAs | 86 | |
| Variant | ||
| Heterozygous SNPsb | 2 009 487 | |
| Annotation | DNA/Protein | |
| Pfam-A accessions | 21 645 | |
| COGsc accessions | 14 049 | |
| InterPro accessions | 66 567 | |
| PANTHERd accessions | 38 868 | |
| ECe numbers | 752 | |
| Ortholog groups | 9856 | |
| Structure feature | ||
| Conserved domain models | 852 248 | |
| Conserved sites | 36 731 | |
| Pathway/Network | ||
| GOf accessions | 37 188 | |
| KOg accessions | 3714 | |
| Metabolic pathway | ||
| Proteins | 3946 | |
| Pathway maps | 191 | |
| PPI | ||
| Proteins | 2202 | |
| Interactions | 34 169 | |
| Comparative genomics | ||
| Best Arabidopsis hits | 16 383 | |
| Best rice hits | 21 849 |
aFPKM: Fragments per kilobase of transcript per million mapped reads.
bHeterozygous SNPs: heterozygous single nucleotide polymorphisms.
cCOGs: Clusters of orthologous group.
dPANTHER: Protein ANalysis THrough Evolutionary Relationships (one classification system of protein).
eEC: Enzyme commission.
fGO: Gene ontology.
gKO: KEGG orthology.