Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse

Background: We previously demonstrated that gene expression profiles during neuronal differentiation in vitro and hippocampal development in vivo were very similar, due to a conservation of the important second singular value decomposition (SVD) mode (Mode 2) of expression. The conservation of Mode 2 suggests that it reflects a regulatory mechanism conserved between the two systems. In either dataset, the expression vectors of all the genes form two large clusters that differ in the sign of the contribution of Mode 2, which for the majority of them reflects the difference between down- or up-regulation. Results: In the current work, we used a novel approach of analyzing cis-regulation of gene expression in a subspace of a single SVD mode of temporal expression profiles. In the putative upstream regulatory sequences identified by mouse-human homology for all the genes represented in either dataset, we searched for simple features (motifs and pairs of motifs) associated with either sign...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Michal Dabrowski, Stein Aerts, Bozena Kaminska
• Keywords: BMCBI 2006, Gene Expression, Hippocampal Development, Mode 2