Our choice to use the software MEGAN for the analysis of the datasets from the Daphnia projects is based on several aspects, which help to reduce known problems in comparative metagenomics.
For differential M. bovis BCG gene and small RNA expression analysis, the datasets derived from enriched infections (IF1/2ER) were compared to a reference culture of exponentially growing M. bovis BCG (EGB).
Sequences used in the phylogenetic analysis include the dataset from [ 33] to which we added sequences from the genomes of Physcomitrella patens and Selaginella moellendorffii retrieved from JGI [ 56].
To test this hypothesis and also to investigate the sulfur effect in an organism other than yeast, we performed PACE analysis of the dataset from Wegener et al. [19].
Also, phylogenetic analysis of the dataset from nucleotide sequences of vaccine strains against reference sequences from GenBank and the strains from the Pasteur Institute showed that all of the RV strains extracted from Fuchsoral and Lysvulpen formed one group of SAD vaccine virus strains based on the analysed fragments of the N and G genes (Fig. 1).
In the pruning analysis, the AUC values for the datasets from all three institutes generally improved according to the number of ADTrees in the prediction model (Appendix E (Additional file 1)).
Concerning gene expression analysis, the integration datasets from diverse platforms in this Next-Generation Genomics era, including genomics, epigenomics, and proteomics with transcriptomics, is critical in the effort to understand complex biological systems.
Hypergeometric distribution statistical analysis [ 44] was applied in the datasets from fruit and leaf to find the sub- and over-estimated GO terms in each species.
After individual analysis of the datasets retrieved from GEO [ 31] and ArrayExpress [ 32] (table 1), the results were combined in an approach called intersections.
Thus, our analysis is based on the dataset from 77 members of the project who were involved in 23,359 tasks associated with 37,323 change sets.
