As a validation of the ALIGATOR results, set-based analysis was also performed on the set of SNPs within each of the GO processes that were significantly enriched in both GWAS datasets.
To obtain a better understanding of the biological functions of the unigenes, a KEGG pathway-based analysis was also performed.
This network-based analysis was also applied to another dataset that documents differences in gene expression between docetaxel-resistant and parental MDA-MB-231 breast cancer cell lines (Gene Expression Omnibus (GEO) accession number GSE28784).
Voxel-based analysis was also performed in a common standard space using the Tract-Based Spatial Statistics (TBSS) methods implemented in FSL (FMRIB, Oxford UK, http://www.fmrib.ox.ac.uk/fsl) (Smith et al., 2006).
Furthermore, this search-based analysis was also particularly important to determine a "bacterial fingerprint" in B. azoricus gill tissues, since we expected the vent mussel to have a rich microorganismal community and more specifically a substantial accumulation of endosymbiont bacteria within its gill tissues.
To identify efficiently nsSNPs related to drought tolerance, SNP based cluster analysis was also carried out using all nsSNPs detected from all tested lines.
While many bacterial genomes exhibit high levels of genetic recombination, S. aureus has previously been shown to be highly clonal [9], [15], and therefore, a minimal spanning network based on maximum parsimony analysis was also conducted.
The association between anti-PGL-I seropositivity and the operational classification of the index leprosy case based on the multivariate analysis was also observed by other authors who performed multivariate analysis [ 13, 17].
Furthermore, participants documented the frequency of pain attacks per day in the same fashion and analysis was also based on the average of the last three days prior to assessment day (e.g., baseline and post-stimulation).
The analysis was also based on new data provided by the Multiple Indicator Survey preliminary report.
