Table 3.
Enriched functional categories in the conserved TE module.
| Name | Number Genes | P-Value | FDR |
|---|---|---|---|
| Histone binding | 11 | 4.74E-05 | 5.54E-03 |
| Protein complex scaffold | 7 | 4.63E-05 | 5.54E-03 |
| Cadherin signaling pathway | 5 | 1.74E-04 | 1.97E-02 |
| Wnt signaling pathway - Mus musculus (mouse) | 9 | 4.76E-05 | 1.41E-02 |
| Adherens junction - Mus musculus (mouse) | 7 | 1.36E-04 | 2.01E-02 |
| Abnormal temporal memory | 10 | 1.26E-05 | 4.48E-02 |
| Abnormal associative learning | 12 | 3.41E-05 | 4.48E-02 |
| Abnormal contextual conditioning behavior | 8 | 1.11E-04 | 4.48E-02 |
| Abnormal nasal bone morphology | 7 | 2.69E-05 | 4.48E-02 |
| Abnormal craniofacial morphology | 30 | 1.07E-04 | 4.48E-02 |
| Craniofacial phenotype | 30 | 1.07E-04 | 4.48E-02 |
| Short nasal bone | 5 | 1.09E-04 | 4.48E-02 |
| Preweaning lethality | 93 | 4.98E-05 | 4.48E-02 |
| Embryonic lethality during organogenesis, complete penetrance | 28 | 5.91E-05 | 4.48E-02 |
| Pale yolk sac | 93 | 6.11E-05 | 4.48E-02 |
| Embryonic lethality during organogenesis | 32 | 8.64E-05 | 4.48E-02 |
| Abnormal neural tube closure | 16 | 9.77E-05 | 4.48E-02 |
| Lethality during fetal growth through weaning | 48 | 1.00E-04 | 4.48E-02 |
Gene-gene coexpression network analysis revealed a group of genes with tightly correlated expression levels which contained a high number of TEs (see text for details on network construction). Roughly this same group of correlated genes and TEs was identified in prefrontal cortex, amygdala, and liver of male C57Bl/6J mice. We submitted the annotated genes within this conserved TE module to WebGestalt (http://www.webgestalt.org) (Wang J. et al., 2017) to determine the enriched pathways, phenotypes and ontologies. Of the 348, 149 Illumina probes were used for analysis, as most probes were mapped to TEs and therefore unannotated and unable to be used for analysis. We used the criteria that the enriched category must include ≥ 3 genes and pass significance threshold of FDR-adjusted hypergeometric p < 0.05. The enriched category is given under the Name column. The number of unique genes contributing to the categorical enrichment and the p-value and FDR value are also provided in the table.