Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice
Abstract
:1. Introduction
2. Materials and Methods
2.1. Expression Data
2.2. Co-Expression Analysis
2.3. Tissue Specificity
2.4. Allele-Specific Expression
2.5. Measures of Sequence Evolution
2.6. Enrichment Analyses
2.7. Protein Interaction Networks
2.8. Variant Annotations
3. Results
3.1. Properties of Gene Connectivity within and Across Tissues
3.2. Tissue Specific Expression and Connectivity
3.3. Relationship between Regulatory Variation and Connectivity
3.4. Relationship between Connectivity and Sequence Evolution
3.5. Constraint on Cross-Tissue Hub Genes
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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dN/dS | SNP Density | |||
---|---|---|---|---|
Variable | Pairwise 1 | Partial 2 | Pairwise | Partial |
Average expression level across tissues | −0.26 *** | −0.15 *** | −0.15 *** | −0.14 *** |
Expression IQR across tissues | −0.22 *** | 0.042 ** | −0.05 *** | 0.17 *** |
Average connectivity across tissues | −0.18 *** | −0.045 *** | −0.16 *** | −0.09 *** |
Connectivity IQR across tissues | −0.12 *** | 0.04 ** | −0.11 *** | −0.04 *** |
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Mack, K.L.; Phifer-Rixey, M.; Harr, B.; Nachman, M.W. Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice. Genes 2019, 10, 225. https://doi.org/10.3390/genes10030225
Mack KL, Phifer-Rixey M, Harr B, Nachman MW. Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice. Genes. 2019; 10(3):225. https://doi.org/10.3390/genes10030225
Chicago/Turabian StyleMack, Katya L., Megan Phifer-Rixey, Bettina Harr, and Michael W. Nachman. 2019. "Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice" Genes 10, no. 3: 225. https://doi.org/10.3390/genes10030225
APA StyleMack, K. L., Phifer-Rixey, M., Harr, B., & Nachman, M. W. (2019). Gene Expression Networks Across Multiple Tissues Are Associated with Rates of Molecular Evolution in Wild House Mice. Genes, 10(3), 225. https://doi.org/10.3390/genes10030225