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Figure 3 | Genome Biology

Figure 3

From: Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks

Figure 3

Validation of ARACNe-predicted Nr3c1/GR regulon by siRNA-mediated downregulation of Nr3c1/GR followed by microarray analysis. (A) Nr3c1/GR was downregulated by use of a synthetic siRNA (Applied Biosystems) in the rat striatal medium spiny neuron cell line M213 relative to an aspecific ‘scrambled’ siRNA (Scr.) control. (B) We performed microarray profiling and used gene expression differences between cells treated with siRNA to Nr3c1/GR and the ‘scrambled’ siRNA control to interrogate the Nr3c1 regulon (that is, targets of Nr3c1/GR predicted by ARACNe) with the Gene Set Enrichment Analysis (GSEA) [23]; n = 4. Results showed enrichment of the genes in the Nr3c1/GR regulon among the genes whose expression is affected by siRNA-mediated downregulation of Nr3c1/GR in M213 cells (GSEA result: NES = 1.28, P <0.004). (C) Sequence logo of Nr3c1/GR binding site from JASPAR database [24].

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Genome Biology

ISSN: 1474-760X

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