The systems genetics resource: A web application to mine global data for complex disease traits

Frontiers in Genetics

Volumn 4, Issue MAY, 2013, Pages

  Van Nas, Atila ^a   Pan, Calvin ^a   Ingram Drake, Leslie A ^a   Ghazalpour, Anatole ^a   Drake, Thomas A ^a   Sobel, Eric M ^a   Papp, Jeanette C ^a   Lusis, Aldons J ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Data analysis; Data integration; Database; Genomics; Systems biology; Web services

Indexed keywords

EID: 84883530603     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2013.00084     Document Type: Article

References (41)

1. Aten, J. E., Fuller, T. F., Lusis, A. J., and Horvath, S. (2008). Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst. Biol. 2:34. doi:10.1186/1752-0509-2-34
2. Bennett, B. J., Farber, C. R., Orozco, L., Kang, H. M., Ghazalpour, A., Siemers, N., et al. (2010). A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res. 20, 281-290.
3. Chen, Y., Zhu, J., Lum, P. Y., Yang, X., Pinto, S., MacNeil, D. J., et al. (2008). Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429-435.
4. Colinayo, V. V., Qiao, J. H., Wang, X., Krass, K. L., Schadt, E., Lusis, A. J., et al. (2003). Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice. Mamm. Genome 14, 464-471.
5. Davis, R. C., Schadt, E. E., Smith, D. J., Hsieh, E. W., Cervino, A. C., van Nas, A., et al. (2005). A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background. Genomics 86, 259-270.
6. Davis, R. C., van Nas, A., Bennett, B. J., Orozco, L., Pan, C., Rau, C. D., et al. (2013). Genome-wide association mapping of blood cell traits in mice. Mamm. Genome 24, 105-118.
7. Davis, R. C., van Nas, A., Castellani, L. W., Zhao, Y., Zhou, Z., Wen, P., et al. (2012). Systems genetics of susceptibility to obesity-induced diabetes in mice. Physiol. Genomics 44, 1-13.
8. Farber, C. R., Bennett, B. J., Orozco, L., Zou, W., Lira, A., Kostem, E., et al. (2011). Mouse genome-wide association and systems genetics identify Asxl2 as a regulator of bone mineral density and osteoclastogenesis. PLoS Genet. 7:e1002038. doi:10.1371/journal.pgen.1002038
9. Farber, C. R., van Nas, A., Ghazalpour, A., Aten, J. E., Doss, S., Sos, B., et al. (2009). An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association. J. Bone Miner. Res. 24, 105-116.
10. Flint, J., and Mackay, T. F. (2009). Genetic architecture of quantitative traits in mice, flies, and humans. Genome Res. 19, 723-733.
11. Furlotte, N. A., Kang, E. Y., Van Nas, A., Farber, C. R., Lusis, A. J., and Eskin, E. (2012). Increasing association mapping power and resolution in mouse genetic studies through the use of meta-analysis for structured populations. Genetics 191, 959-967.
12. Gargalovic, P. S., Imura, M., Zhang, B., Gharavi, N. M., Clark, M. J., Pagnon, J., et al. (2006). Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc. Natl. Acad. Sci. U.S.A. 103, 12741-12746.
13. Ghazalpour, A., Bennett, B., Petyuk, V. A., Orozco, L., Hagopian, R., Mungrue, I. N., et al. (2011). Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet. 7:e1001393. doi:10.1371/journal.pgen.1001393
14. Ghazalpour, A., Doss, S., Kang, H., Farber, C., Wen, P. Z., Brozell, A., et al. (2008). High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet. 4:e1000149. doi:10.1371/journal.pgen.1000149
15. Ghazalpour, A., Doss, S., Sheth, S. S., Ingram-Drake, L. A., Schadt, E. E., Lusis, A. J., et al. (2005). Genomic analysis of metabolic pathway gene expression in mice. Genome Biol. 6, R59.
16. Ivandic, B. T., Qiao, J. H., Machleder, D., Liao, F., Drake, T. A., and Lusis, A. J. (1996). A locus on chromosome 7 determines myocardial cell necrosis and calcification (dystrophic cardiac calcinosis) in mice. Proc. Natl. Acad. Sci. U.S.A. 93, 5483-5488.
17. Kang, H. M., Zaitlen, N. A., Wade, C. M., Kirby, A., Heckerman, D., Daly, M. J., et al. (2008). Efficient control of population structure in model organism association mapping. Genetics 178, 1709-1723.
18. Keller, M. P., and Attie, A. D. (2010). Physiological insights gained from gene expression analysis in obesity and diabetes. Annu. Rev. Nutr. 30, 341-364.
19. Langfelder, P., Castellani, L. W., Zhou, Z., Paul, E., Davis, R., Schadt, E. E., et al. (2012). A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models. Biochim. Biophys. Acta 1821, 435-447.
20. MacLellan, W. R., Wang, Y., and Lusis, A. J. (2012). Systems-based approaches to cardiovascular disease. Nat Rev Cardiol 9, 172-184.
21. Martin, L. J., Lau, E., Singh, H., Vergnes, L., Tarling, E. J., Mehrabian, M., et al. (2012). ABCC6 localizes to the mitochondria-associated membrane. Circ. Res. 111, 516-520.
22. Meng, H., Vera, I., Che, N., Wang, X., Wang, S. S., Ingram-Drake, L., et al. (2007). Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics. Proc. Natl. Acad. Sci. U.S.A. 104, 4530-4535.
23. Meng, Q., Makinen, V. P., Luk, H., and Yang, X. (2013). Systems biology approaches and applications in obesity, diabetes, and cardiovascular diseases. Curr. Cardiovasc. Risk Rep. 7, 73-83.
24. Orozco, L. D., Bennett, B. J., Farber, C. R., Ghazalpour, A., Pan, C., Che, N., et al. (2012). Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages. Cell 151, 658-670.
25. Orozco, L. D., Cokus, S. J., Ghazalpour, A., Ingram-Drake, L., Wang, S., van Nas, A., et al. (2009). Copy number variation influences gene expression and metabolic traits in mice. Hum. Mol. Genet. 18, 4118-4129.
26. Park, C. C., Gale, G. D., de Jong, S., Ghazalpour, A., Bennett, B. J., Farber, C. R., et al. (2011). Gene networks associated with conditional fear in mice identified using a systems genetics approach. BMC Syst. Biol. 5:43. doi:10.1186/1752-0509-5-43
27. Parks, B. W., Nam, E., Org, E., Kostem, E., Norheim, F., Hui, S. T., et al. (2013). Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab. 17, 141-152.
28. Romanoski, C. E., Che, N., Yin, F., Mai, N., Pouldar, D., Civelek, M., et al. (2011). Network for activation of human endothelial cells by oxidized phospholipids: a critical role of heme oxygenase 1. Circ. Res. 109, e27-e41.
29. Romanoski, C. E., Lee, S., Kim, M. J., Ingram-Drake, L., Plaisier, C. L., Plaisier, C. L., et al. (2010). Systems genetics analysis of gene-by-environment interactions in human cells. Am. J. Hum. Genet. 86, 399-410.
30. Schadt, E. E., Lamb, J., Yang, X., Zhu, J., Edwards, S., Guhathakurta, D., et al. (2005). An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet. 37, 710-717.
31. Schadt, E. E., Monks, S. A., Drake, T. A., Lusis, A. J., Che, N., Colinayo, V., et al. (2003). Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297-302.
32. Stancáková, A., Civelek, M., Saleem, N. K., Soininen, P., Kangas, A. J., Cederberg, H., et al. (2012). Hyperglycemia and a common variant of GCKR are associated with the levels of eight amino acids in 9,369 Finnish men. Diabetes 61, 1895-1902.
33. Suwanwela, J., Farber, C. R., Haung, B. L., Song, B., Pan, C., Lyons, K. M., et al. (2011). Systems genetics analysis of mouse chondrocyte differentiation. J. Bone Miner. Res. 26, 747-760.
34. Terra, J. K., France, B., Cote, C. K., Jenkins, A., Bozue, J. A., Welkos, S. L., et al. (2011). Allelic variation on murine chromosome 11 modifies host inflammatory responses and resistance to Bacillus anthracis. PLoS Pathog. 7:e1002469. doi:10.1371/journal.ppat.1002469
35. van Nas, A., Guhathakurta, D., Wang, S. S., Yehya, N., Horvath, S., Zhang, B., et al. (2009). Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology 150, 1235-1249.
36. van Nas, A., Ingram-Drake, L., Sinsheimer, J. S., Wang, S. S., Schadt, E. E., Drake, T., et al. (2010). Expression quantitative trait loci: replication, tissue- and sex-specificity in mice. Genetics 185, 1059-1068.
37. Wang, S., Yehya, N., Schadt, E. E., Wang, H., Drake, T. A., and Lusis, A. J. (2006). Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet. 2:e15. doi:10.1371/journal.pgen.0020015
38. Wang, S. S., Schadt, E. E., Wang, H., Wang, X., Ingram-Drake, L., Shi, W., et al. (2007a). Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data. Circ. Res. 101, e11-e30.
39. Wang, S. S., Shi, W., Wang, X., Velky, L., Greenlee, S., Wang, M. T., et al. (2007b). Mapping, genetic isolation, and characterization of genetic loci that determine resistance to atherosclerosis in C3H mice. Arterioscler. Thromb. Vasc. Biol. 27, 2671-2676.
40. Yang, X., Deignan, J. L., Qi, H., Zhu, J., Qian, S., Zhong, J., et al. (2009). Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat. Genet. 41, 415-423.
41. Yang, X., Schadt, E. E., Wang, S., Wang, H., Arnold, A. P., Ingram-Drake, L., et al. (2006). Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res. 16, 995-1004.