%0 Journal Article
%T Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation
%A Tamara Aid-Pavlidis
%A Pavlos Pavlidis
%A T£¿nis Timmusk
%J BMC Genomics
%D 2009
%I BioMed Central
%R 10.1186/1471-2164-10-420
%X In our study, we performed meta-coexpression analysis of publicly available microarray data using BDNF as a "guide-gene" introducing a "subset" approach. The key steps of the analysis included: dividing datasets into subsets with biologically meaningful sample content (e.g. tissue, gender or disease state subsets); analyzing co-expression with the BDNF gene in each subset separately; and confirming co- expression links across subsets. Finally, we analyzed conservation in co-expression with BDNF between human, mouse and rat, and sought for conserved over-represented TFBSs in BDNF and BDNF-correlated genes. Correlated genes discovered in this study regulate nervous system development, and are associated with various types of cancer and neurological disorders. Also, several transcription factor identified here have been reported to regulate BDNF expression in vitro and in vivo.The study demonstrates the potential of the "subset" approach in co-expression conservation analysis for studying the regulation of single genes and proposes novel regulators of BDNF gene expression.The accumulation of genome-wide gene expression data has enabled biologists to investigate gene regulatory mechanisms using system biology approaches. Recent developments in microarray technologies and bioinformatics have driven the progress of this field [1]. Moreover, publicly available microarray data provide information on human genome-wide gene expression under various experimental conditions, which for most researchers would be difficult to access otherwise.BDNF (brain-derived neurotrophic factor) plays an important role in the development of the vertebrates' nervous system [2]. BDNF supports survival and differentiation of embryonic neurons and controls various neural processes in adulthood, including memory and learning [3], depression [4], and drug addiction [5]. Alterations in BDNF expression can contribute to serious pathologies such as epilepsy, Huntington, Alzheimer's, and Parkinson's dis
%U http://www.biomedcentral.com/1471-2164/10/420