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Data summary

Table 1. BambooGDB data content and statistics as 12 August 2013
Data Set Data Type Data Statistics
Basic Data content DNA/Protein Genes 31,987
Expressed genes (FPKM1≥1) 28,576
MiRNA target genes 161
Proteins 31,987
RNA tRNAs 1,167
MicroRNAs 86
Variant Heterozygous SNPs2 2,009,487
Annotation DNA/Protein Pfam-A accessions 21,645
COG3 accessions 14,049
InterPro accessions 66,567
PANTHER4 accessions 38,868
EC5 numbers 752
Ortholog Groups 9,856
Structure feature
Conserved domain models 852,248
Conserved sites 36,731
Pathway/Network GO6 accessions 37,188
KO7 accessions 3,714
Metabolic pathway
Genes/proteins 3,946
Pathway maps 191
Protein-protein interaction
Proteins 2,202
Interactions 34,169
Comparative genomics Best Arabidopsis hits 16,383
Best rice hits 21,849

1. FPKM: Fragments Per Kilobase of transcript per Million mapped reads

2. Heterozygous SNPs: Heterozygous Single Nucleotide Polymorphisms

3. COG: Clusters of Orthologous Group

4. PANTHER: Protein ANalysis THrough Evolutionary Relationships, one classification system of protein

5. EC: Enzyme Commission

6. GO: Gene Ontology

7. KO: KEGG Ortholog



Table 2: 7 plant genomes using in BambooGDB database
No. Species name Common name Taxonomy Release version Genome size(Mb) Gene loci number Access Reference
1 Arabidopsis thaliana Arabidopsis Arabidopsis TAIR 10 135 27416 TAIR Nature
2 Brachypodium distachyon Purple false brome Grass Version 1.0 272 26552 Brachypodium.org Nature
3 Panicum virgatum switchgrass Grass Version 0.0(only contigs) 1358 65878 JGI -
4 Oryza sativa Rice Grass RAP 2.0 (Nov 2007) 372 55986 RAP Nature
5 Sorghum bicolor Sorghum Grass Sbi 1.4 697 34496 JGI Nature
6 Setaria italica Foxtail millet Grass Version 2.1 405.7 35471 JGI -
7 Zea mays Maize Grass Release 5b 2066 39656 AGI Science

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