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These proteins were classified by their annotated function on the KEGG pathway.
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Genes induced by multiple-stress condition were clustered by their annotated functions in response to three different stresses reported previously (nutrient starvation [21], acidic shock [22] and hypoxic treatment [39]).
Below we consider differentially expressed genes in W. smithii that, by virtue of their annotated function in D. melanogaster, are involved in post-diapause morphogeneis, or in the transition from potentially oxygen-poor winter diapause environments to oxygen-rich spring environments conducive to active development.
To verify RNA-seq data, three up- and downregulated genes were selected based on their annotated function from each tissue and analysed by quantitative reverse transcription PCR (qRT-PCR, Figure 5, Additional file 8: Table S2).
Genes have been clustered together, manually, based on their annotated function in the Saccharomyces Genome Database (SGD).
Those hits with gene names were then investigated for their annotated function through database searching at the PANTHER (Protein ANalysis THrough Evolutionary Relationships, http://www.pantherdb.org) classification system.
The protein-coding genes were ranked according to their maximal expression level in any stage, and broadly categorized according to their annotated function.
Although there is no guarantee that all genes in GI will be deletable without detrimental effects, by looking at their annotated functions it is possible to have a clue of their role in the cell.
Genes found to be significantly differentially expressed in wild type sporozoites compared to mixed blood stages were placed into functional categories based on their annotated functions.
Those proteins and their annotated functions are listed in Table 3.
The differentially expressed genes were classified into groups based on their annotated functions using the BGSSJ software tool [ 63].
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