Among 16th-century readers was the French essayist Michel de Montaigne, who filled his copy with annotations, including one suffused with obvious delight: "Since the movements of the atoms are so varied, it is not unbelievable that the atoms once came together in this way, or that in the future they will come together like this again, giving birth to another Montaigne".
Homologs to other bacterial species were also identified with annotations including: Cu-Zn superoxide dismutase, excinuclease, chaperone protein DnaK, SecY subunit, zinc transporter, and cation efflux protein.
This set also has a high percentage of genes in the Signaling category, with annotations including products such as annexin, cytochrome P450, nucleoside diphosphate kinase, and protein phosphatase.
Those genes that have sustained alterations in expression were over-represented in genes with annotations including control of apoptosis, oxidative stress, and xenobiotic metabolism (additional file 2).
For each gene the top BLAST hit (E-value of ≤10E-4) with annotation including the experimentally tested phenotypes was extracted (Additional file 1: Table S5 and Additional file 2).
From this analysis, levels of sophistication with respect to the types and extent of annotations included were identified.
For example, in glycolysis, there was no pyruvate kinase included in the early versions of the model, because none of the existing genome annotations included a gene with this annotated function.
Sequences and transcript abundances of all annotated T. amboinensis genes are available along with detailed functional annotations, including GO, protein domains, and metabolic pathways (see Data Availability).
Those sequences with their functional annotations, including GO terms and domain similarity related description, are also provided as Additional file 1: 'Cape gooseberry cDNAs'.
Each family is associated with rich functional and structural annotations include Gene Ontology [ 62], pathways and more.
Of the 44 probes, 30 were associated with genes that had functional annotations including a gene symbol (using the hgug4112a annotation package for Bioconductor, version 2.2.11).
