DWE: discriminating word enumerator.

Motivation: Tissue-specific transcription factor binding sites give insight into tissue-specific transcription regulation.

Results: We describe a word-counting-based tool for de novo tissue-specific transcription factor binding site discovery using expression information in addition to sequence information. We incorporate tissue-specific gene expression through gene classification to positive expression and repressed expression.

Identifying combinatorial regulation of transcription factors and binding motifs.

Background: Combinatorial interaction of transcription factors (TFs) is important for gene regulation. Although various genomic datasets are relevant to this issue, each dataset provides relatively weak evidence on its own. Developing methods that can integrate different sequence, expression and localization data have become important.

Transcription factor binding element detection using functional clustering of mutant expression data.

As a powerful tool to reveal gene functions, gene mutation has been used extensively in molecular biology studies. With high throughput technologies, such as DNA microarray, genome-wide gene expression changes can be monitored in mutants. Here we present a simple approach to detect the transcription-factor-binding motif using microarray expression data from a mutant in which the relevant transcription factor is deleted.

Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.

Proteins comprising the core of the eukaryotic cellular machinery are often highly conserved, presumably due to selective constraints maintaining important structural features. We have developed statistical procedures to decompose these constraints into distinct categories and to pinpoint critical structural features within each category. When applied to P-loop GTPases, this revealed within Rab, Rho, Ras, and Ran a canonical network of molecular interactions centered on bound nucleotide.