Downregulation of DNA-binding of the p50 homodimer and NF-κB in alcoholics may result in changes in expression of genes that are regulated through κB elements, binding sites for these transcription factors. To test this hypothesis we used a computational approach to compare the number of genes containing κB elements in two sets of genes that were previously identified by one of the co-author groups [14] as downregulated (n = 270) or upregulated (n = 209) in the PFC of alcoholics (Table S1). A group of 1164 genes that were randomly selected from the set, which did not include genes differentially expressed in alcoholics, was studied for comparison (control genes; Table S1). Previous analyses human chromosome 22 with chromatin immunoprecipitation and genomic microarrays [50] demonstrated that κB elements are enriched at the 5′-end of genes. Therefore, we focus on the identification of κB elements in 10 kb-promoter regions. p50 homodimer and NF-κB bind to virtually the same κB elements. Weight matrix for NF-κB in the JASPAR database [42] consists of sequences of the “NF-κB”-subtype that are also targets for the p50
