Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor

Genetic networks of cooperative redox regulation of osteopontin

“…Using a smaller dataset, we previously identified brainderived neurotrophic factor (Bdnf), interleukin 6 and proliferin as strong predictors of opn (Johnson et al, 2004). Because a different set of predictors was identified in the more comprehensive analysis described here, pathway network searches were conducted using a pooled set to uncover regulated interactive networks for these genes.…”

“…Thus, identity differences among predictor genes are accounted for by functional connectivity among genes within the network and likely secondary to differences in the size of datasets. Our previous analysis was based on the expression of 200 genes across 40 different Affymetrix arrays from three different tissues (Johnson et al, 2004), while the current study used a more diversified data resource that included 235 microarrays from different biological models. To maximally identify closely regulated interactive networks for opn predictor genes, we pooled the gene sets from both studies to construct signaling pathway networks.…”

“…Statistical documentation can be found in reference (Johnson et al, 2004;Ramos et al, 2007). After chip normalization, the mean (x), standard deviation (sd) and coefficient of variation cv = sd/x were calculated for each gene across all samples, and the intensity level (x) for each gene was standardized across all arrays by x = x − x/sd.…”

“…The data were derived from internal and external databases. Internal datasets were described in detail in Johnson et al (2004) and Thackaberry et al (2005). The downloadable data from http:// cardiogenomics.med.harvard.edu/groups/proj1/pages/download_ home1.html were related to a mouse model of myocardial infarction.…”

Exposure to persistent organic pollutants as potential risk factors for developing diabetes

“…Croutch et al [102] administered TCDD and HxCDD to rats and measured the levels of circulating insulin, glucose, and IGF-I, as well as hepatic levels of phos-phoenolpyruvate carboxykinase (PEPCK) mRNA expression, and found that both TCDD and HxCDD inhibit IGF-I, with less inhibition of PEPCK, and attributed the weight loss seen in the animals to these actions, but no changes in levels of either insulin or glucose were observed. Johnson et al [103] reported a genes' network showing interactions between the AhR, cytochrome P450 1B1, IGF-binding protein-5 (IGFBP-5), lysyl oxidase, and osteopontin [59]. Some studies have focused on specific genes.…”