The speciation of each of these elements is significantly pH dependent.
In the analysis of the parents grown with the BaySha populations, nine of the elements measured, Na, Mg, P, K, Ca, Ni, Zn, Mo and Cd, were significantly different in both growing conditions, two were not significantly different in either condition, and eight elements were significantly different in only one condition (Tables 4 and 5, Table S2).
Indeed, the same statistical test we applied to the mouse data revealed that in both HsM1 and HsM2, the 10% most highly induced putative targets of each of the two elements were significantly enriched for genes whose promoter contained a signature for both NF-κB and ISRE (Table 6).
The P1BS cis-acting elements were significantly overrepresented in the 1-kb upstream region of transcripts upregulated in root and shoot at late –P stress (Table 2).
Instead of G-boxes, we found that W-boxes and OCS elements were significantly overrepresented in the upstream 500 bp region in the blue light-induced genes that were dependent on both cry1 and HFR1.
Further examination of the SINE elements showed that only Alu family elements were significantly enriched when compared to the genome average, with 20 of the 40 flanking regions intersecting a known Alu element (p<0.008 from 1000 simulations, see Figure 3).
While many elements were significantly correlated within each of the five experiments, only three pairs of elements were correlated in every population×environment we analyzed: Li-Na, Mg-Ca, and Cu-Zn, although Li-As, Li-Cd, Li-K, Li-Zn, P-Fe, Mg-Zn and Zn-Cd were found in 4 of the 5 experiments (Figure 1).
Silva et al. [11] found that mir SINE and L2 LINE elements were significantly more conserved that expected between humans and mouse, whereas Lowe et al. [13] found that more than 50% of all TE derived CNG nucleotides come from LINEs, with ∼25% coming from SINEs and a small proportion from LTR and DNA elements.
