Comparisons of gene expression within the groups of vaccinated and naïve fish found large scale differences between HR and LR.
Non-metric multidimensional scaling analysis reveals large-scale differences between the sister taxa S. frontalis and S. attenuata and the rest of the Delphininae.
Having demonstrated large-scale differences between the rat and mouse transcriptional responses to TCDD and having shown that these differences lead to alterations in specific pathways, we next considered mechanism.
Gene-centric analyses, as discussed above, allow construction of functional scaffolds to model metabolic interactions within a community (e.g. Warnecke et al., 2007) as well as the determination of large-scale differences between the gene complements of distinct ecosystems (e.g. Tringe et al., 2005; DeLong et al., 2006; Dinsdale et al., 2008a).
Freely dissolved and crayfish tissue PAH concentrations were standardized to total sample PAH concentration (ΣPAH) and 4th root transformed prior to PCA because preliminary tests indicated that this transformation improved overall data visualization and reduced the impact of large scaling differences between PAH proportions.
Comparisons of Btau4.6 and UMD3.1 to BtOM1.0 also revealed large-scale difference between these sequence assemblies.
We corrected for differences in normal tissue contamination then calculated a Z score for the presence of large-scale differences between samples, as described in the Supplementary Methods file and Supplementary Figure 4. Seven pairs of tumours stood out as being significantly different (H08, H09, H10, H13, H14, H15 and H19; Supplementary Table 6).
Most of the differentially expressed genes on the microarray were not related to sex function, suggesting large scale differences in gene expression between the sexes are present early in development.
Given the high habitat heterogeneity and environmental variability in these canyons and channels, we hypothesise that the nematode assemblages will be largely controlled by small-scale, local environmental conditions rather than large-scale differences between canyons or water depths.
