[show abstract][hide abstract] ABSTRACT: Alzheimer’s disease is the most common form of dementia affecting millions of older people world wide. Identification of transcriptional factor binding sites of disease specific co-expressed genes and the possible transcriptional regulation of the genes will lead to a better understanding of complex diseases such as Alzheimer’s disease. However, the regulatory mechanisms driving thesechanges, in particular the networks of transcription factors involved, is not fully understood to date. The computational identification of conserved TFBS in the regulatory regions of hundreds of genes at a time especially suited for microarray gene expression datasets. We report clusters of co-expressed genes and the identification of conserved TFBSs using microarray gene expression data sets. We investigated microarray gene expression data from Gene Expression Omnibus (GEO) specific to Alzheimer’s disease. The dataset consists of 14 normal and 14 Alzheimer disease samples. Differential expression analysis results 240 differentially expressed genes which are more significant. Hierarchical clustering of these significance genes shows eight clusters of co-expressed genes. The detection of over-represented transcription factor binding sites in the promoters regions of co-expressed genes reveals transcription factor binding site classes ZEB1, MZF1 1-4, ZNF354C, ELF5 and SPIB in upstream ofhuman promoter and responsible for apoptosis.