Supplemental Data
Files in this Data Supplement:
- Supplemental file 4 (.pdf, 328 KB) - Supplemental file 4 contains Supplemental tables (1-4), with lists of pathways significantly enriched with genes differentially expressed upon fasting in four metabolically highly active organs (small intestine, kidney, liver and muscle). The pathway analysis is performed in the MetaCoreTM suit.
- Supplemental figure 1 (.pdf, 168 KB) - Supplemental figure 1. ��-hydroxybutyrate concentration in intestinal perfusates from up to 48h-fasted mice.
- Supplemental file 1 (.pdf, 172 KB) - Supplemental file 1 contains descriptions of Supplemental files and figures and Supplemental experimental procedures.
- Supplemental figure 2 (.pdf, 238 KB) - Supplemental figure 2. Panel A: Correlation plot for liver mRNA expression of FoxO1 and fasting plasma glucose concentrations (left) and lean body mass (right) in the mouse BxD genetic reference population (n=7) as found at www.genenetwork.org and described in the Supplemental Experimental procedures. Panel B: FoxO1 gene expression (upper left panel) varies significantly in the liver of 43 different mice of the BxD RI panel. The normal probability plot (upper right panel) is a graphical technique for assessing whether or not a data set is approximately normally distributed (The data are plotted against a theoretical normal distribution in such a way that the points should form an approximately straight line). Middle and lower panels represent the fasting plasma glucose concentration and body weight, respectively, accompanied by the corresponding normal probability plots.
- Supplemental file 7 (.xls, 69 KB) - Supplemental file 7: the outcome of a complementary, directed text-mining analysis - performed to identify fasting-related genes from the set of differentially expressed genes - is shown in this file. The genes are filtered based on the literature co-occurrence with the keywords 'fasting', 'caloric restriction', 'cachexia', and 'food deprivation'.
- Supplemental file 6 (.xls, 108 KB) - Supplemental file 6: the enriched keywords from the initial CoPub analysis were grouped into higher-order categories (shown in the first worksheet) and an additional enrichment analysis was performed for these new categories for each of the organs (shown in separate worksheets).
- Supplemental file 3 (.xls, 2.9 MB) - Supplemental file 3 contains lists of all the differentially expressed genes in five organs at four fasting conditions in separate worksheets. For each gene, gene symbol, Entrez ID, GenBank accession number, UniGene ID and gene description are provided, followed by the fold change for each of the time points of fasting and the significance of the change (no significance (0), significant upregulation (+1) or downregulation (-1)).
- Supplemental file 10 (.xls, 76 KB) - Supplemental file 10: contains lists of TFs highly interconnected in each of the organs in fasting, which were obtained by using Interactome analysis in MetaCore.
- Supplemental file 5 (.xls, 50 KB) - Supplemental file 5: text-mining analysis was performed using CoPub. The file contains keywords significantly associated with the set of differentially expressed genes in each of the five organs after fasting.
- Supplemental files 8 and 9 (.xls, 81 KB) - Supplemental file 9: the file contains the lists of networks built for five different organs using transcription factor-target modeling in MetaCoreTM suite. A list of top-scoring networks linking the most important transcription factors in the data set with the genes they regulate is shown for each of the organs.
- Supplemental files 8 and 9 (.xls, 57 KB) - Supplemental file 8 contains the lists of networks built for fasted brain, intestine, kidney, liver, and muscle using network analyses for transcriptional regulation in MetaCoreTM suite. A separate network for each transcription factor emerging from our fasting data was built for each of the tissues.
- Supplemental file 2 (.xls, 44 KB) - Supplemental file 2 contains the GO processes enriched in gene sets from 10 clusters shown in Figure 2.