Supplementary information
From the following article:
Variations in DNA elucidate molecular networks that cause disease
Yanqing Chen, Jun Zhu, Pek Yee Lum, Xia Yang, Shirly Pinto, Douglas J. MacNeil, Chunsheng Zhang, John Lamb, Stephen Edwards, Solveig K. Sieberts, Amy Leonardson, Lawrence W. Castellini, Susanna Wang, Marie-France Champy, Bin Zhang, Valur Emilsson, Sudheer Doss, Anatole Ghazalpour, Steve Horvath, Thomas A. Drake, Aldons J. Lusis & Eric E. Schadt
Nature 452, 429-435(27 March 2008)
doi:10.1038/nature06757
Supplementary Information
The file contains Supplementary Discussion, Supplementary Notes, Supplementary Figures 1-11 and Legends and Supplementary Tables 1-2
The Supplementary Discussion and Supplementary Figures 7-9 provide details on inferring causal relationships for traits under feedback control. In addition, the Supplementary Discussion and Supplementary Figures 1 and 2, additional information on Tnfsf4 and Apoa2 expression in the BXH cross. Supplementary Figures 3-5 provide the coexpression networks, enrichments, and characteristics that are critical to the results in the main text. Supplementary Figure 6 provides details on the oral glucose tolerance test carried out on the Ppm1l knockout mice. Supplementary Figure 10 provides details on the Ppm1l knockout construct. Supplementary Figure 11 provides details on the selection of the p-value threshold used to construct the liver and adipose coexpression networks
Supplementary Table 3
The file contains Supplementary Table 3 which lists genes contained in the macrophage-enriched network described in the main text.
Supplementary Table 4
The file contains Supplementary Table 4. The file includes series of indicators for each gene in the macrophage enriched network listed in Supplementary Table 3 that indicate whether a given gene in this network was annotated as belonging to an inflammatory pathway; expressed in macrophage-related tissues; a member of the diet-induced obesity, Zfp90, Alox5, or Pparg perturbation gene expression signatures; or supported as causal for any of the metabolic traits.
Supplementary Table 5
The file contains Supplementary Table 5 For each gene in the macrophage-enriched metabolic network that was supported as causal for at least one metabolic trait, this table provides the number of metabolic traits a given gene was supported as causal for.
Supplementary Table 6
The file contains Supplementary Table 6 which includes the list of genes comprising each module in the liver coexpression network described in the text and depicted in Supplementary Figure 3A.
Supplementary Table 7
The file contains Supplementary Table 7 which lists genes and annotations represented on the microarray used to profile the BXH cross tissues.
Supplementary Methods
This file includes Supplementary Methods. This file was uploaded on 2nd April 2008.
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