Interestingly, although we found concordance between dieldrin and Ni2+ and between diazinon and dieldrin for the ionotropic glutamate receptors, the correlation was much poorer between dieldrin and Ni2+; this points out that the concordance patterns between any two agents can involve sets of genes different from those generating the concordance between one of those agents and a third compound.
The concordance between patterns involving the 123 gene duplicates in that study, and the 1211 plus mito-sensitive nuclear genes in this study, both in terms of chromosomal distribution away from the X, and in terms of tendency for testes-specific expression, is strong; and supports the idea that male-specific mitochondrial mutation loads might underpin these patterns.
For instance, breakdown in phylogenetic concordance patterns has been argued to be partly the result of genetic introgression and hybridization across different fig species [ 8, 38, 40].
To assess the concordance of expression pattern by RNA-Seq and microarrays, all genes expressed by RNA-Seq were evaluated as to whether they were identified as expressed in all microarrays, a subset of microarrays or not represented on the microarray.
By considering different assumptions about spatial bias, we can assess the concordance of spatial patterns between AOD and PM2.5 and investigate the assumption that the spatial pattern in AOD represents signal that is informative about PM2.5.
A key issue in phylogeography and biogeography is the concordance of geographic patterns across taxa.
For example, in the USA female lung cancer mortality maps are consistent with a cohort effect of decreasing exposure by age [ 15], but the concordance between geographical patterns of smoking prevalence and lung cancer is less pronounced for females than for males [ 16].
Based on the concordance between these patterns, an activation Z-score was assigned by IPA after correcting for cases where the regulation directions of the dataset and downstream causal edges are skewed, enabling us to infer whether a given upstream regulator was in an activated state (bias-corrected Z-score > 2), an inhibited state (bias-corrected Z-score < −2), or an uncertain state [ 35].
In the case of UIP (usual interstitial pneumonia) pattern, the concordance was 10/15 (66%).
Because we were interested in the concordance of spatial abnormality patterns and corresponding standard normal deviate relative to controls, SPM-derived mean z-scores were extracted from multiple significant clusters (thresholded at p < 0.001, uncorrected for multiple comparisons [cluster size ≥ 10]).
