Coexpression between gatekeeper genes and ASCOM component <i>Wdr5</i>.

<p>Coexpression patterns observed in both controls and exposed samples support a role for a gatekeeper mechanism. Given the dynamic nature of histone methylation, perturbation cannot be inferred from differences between control and exposed groups. More in-depth studies are warranted to investigate exposure effects on these mechanisms. <b>A:</b> In control samples from Experiment 2 <i>Kdm1</i> was observed to have coexpression higher than the study cut-off limits with only three other histone modifiers including the gatekeeper genes <i>Ehmt1 and Prdm2</i>(approaching significance), and no nuclear receptors. In contrast, in samples from the same experiment that are derived from decedents of an F0 vinclozolin exposed dam, <i>Kdm1</i> showed strong coexpression with <i>Esr2</i>, multiple other nuclear receptors and histone modifiers including the core ASCOM component <i>Wdr5</i> and the methyltransferase <i>Dnmt1</i>. <b>B:</b> In Experiments 3 and 4 <i>Wdr5</i> is anti-correlated with <i>Esr1</i> and has correlated expression with <i>Kdm1</i>. In control samples of Experiment 3 <i>Wdr5</i> shows coexpression approaching significance with <i>Esr1</i> (p = 0.06) and the gatekeeper gene <i>Prdm2</i>. In Experiment 4 only one gatekeeper gene <i>Ehmt1</i> shows coexpression with <i>Wdr5</i>. <b>C:</b> In Experiment 6 <i>Wdr5 showed similar coexpression with Esr2, Ehmt2 and Kdm1</i> in both control and exposed samples and with additional gatekeeper genes in the exposed group. Pink ellipses = nuclear receptors, green = histone methyltransferase and blue = histone demethylase. Edges represent Pearson correlation; some of these relationships were approaching significance as indicated by the associated p-values.</p

Genes down-regulated in F1–F3 generation following vinclozolin exposure, adjusted p-value<0.05.

<p>Genes down-regulated in F1–F3 generation following vinclozolin exposure, adjusted p-value<0.05.</p

Coexpression patterns in human, mouse and rat testis.

<p>Coexpression between ASCOM genes in rat human and mouse are represented as networks. Green octagons = methyltransferases and purple vee = histone demethylases. Edge labels represent Pearson correlation significant at p<0.05.</p

Gatekeeper gene coexpression patterns from Experiment 6.

<p><b>A:</b> Coexpression between genes implicated in the gatekeeper mechanism identified by Garcia- Bassets et al are represented as a network. Pink ellipses = nuclear receptors, yellow and olive green = histone methyltransferases and blue vee = histone demethylase. Edge labels = Pearson correlation significant at p<0.05. <b>3.B:</b> The coexpression relationships in <b>3.A</b> are reflected in the coexpression patterns between gatekeeper genes and genes relevant to endocrine disruptor phenotypes: sexual differentiation (<i>Dmrt1</i>, <i>Dmrta1</i>, <i>Fgf9</i>, <i>Shh</i>, <i>Insl3</i>); embryonic development (<i>Hoxa10</i>), <i>steroidogenesis (Cyp17a1, Star);obesity (Leprot) and</i> spermatogenesis (<i>Prm2</i>).</p

Genes down-regulated in grouped controls v grouped exposed samples following vinclozolin exposure, adjusted p-value<0.05.

<p>Genes down-regulated in grouped controls v grouped exposed samples following vinclozolin exposure, adjusted p-value<0.05.</p

Bland-Altman plot of serum 25(OH)D concentrations at laboratory B (LC-MS/MS) <i>v</i> certified laboratory (LC-MS/MS).

<p>The solid lines indicate the mean bias and the dotted lines indicate the 95% limits of agreement. 25(OH)D, 25-hydroxyvitamin D.</p

Additional file 7: Table S4. of Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration

Unfiltered enriched GO terms associated with miR-223 predicted target genes sourced from Targetscan Fish database. Table contains each GO category and p-value. (XLSX 9 kb

Bland-Altman plot of serum 25(OH)D concentrations at laboratory A (LC-MS/MS) <i>v</i> certified laboratory (LC-MS/MS).

<p>The solid lines indicate the mean bias and the dotted lines indicate the 95% limits of agreement. 25(OH)D, 25-hydroxyvitamin D.</p

Estimates of vitamin D deficiency based on results reported by the certified laboratory and laboratories A-C.

<p>Total deficiency <50 nmol/L. *Given that the general consensus is to exclude 3-epi-25(OH)D₃ when assessing vitamin D status, values for 3-epi-25(OH)D₃ from the certified laboratory were excluded.</p

Social justice in translation: subjectivity, identity, and Occidentalism

Volcano plot of differential gene expression in zebrafish retina after optic nerve crush. Each probe on the array is represented by a single dot, with red dots signifying the 804 differentially expressed transcripts. P- values are presented as –log10 values, expression differences presented as log2 fold changes. We set cut off limits at p < 0.05 and absolute fold change ≥1.5. By these parameters, 459 transcripts were over-expressed and 198 were under-expressed after optic nerve injury. (TIFF 64 kb