Abstract

Regulation of gene expression influences almost all biological processes in an organism, and sequence-specific DNA -binding transcription factors are critical to this control. These transcription factors are involved in complex circuits of regulation between transcription factors and target genes (Babu et al., 2004). Transcription factors that bind specific DNA sequences are arguably the core information-carrying molecules in regulatory networks, and are therefore of particular interest in understanding the evolution of organismal complexity.

However, for most genomes, the repertoire of transcription factors is only partially known. To fill this void, we have developed a novel transcription factor identification method, providing genome-wide transcription factor predictions for organisms from across the tree of life, available at www.transcriptionfactor.org (Kummerfeld & Teichmann, 2006).

By integrating annotated transcription factors with expression data, we have started to gain insight into the dynamics of transcription factor expression under different cellular conditions in a unicellular organism (Luscombe et al,. 2004) and in different developmental stages and tissues in a multi-cellular organism. Both analyses reveal the importance of combinatorial action of transcription factors to determine the state of a cell, and the role of ubiquitous transcription factor hubs.