DiRE -- distant regulatory elements
What you can do:
Identify distant regulatory elements of co-expressed genes.
Highlights:
- Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors and silencers.
- We have developed a web server named DiRE, based on the Enhancer Identification (EI) method, for predicting distant regulatory elements in higher eukaryotic genomes, namely for determining their chromosomal location and functional characteristics.
- The server uses gene co-expression data, comparative genomics and profiles of transcription factor binding sites (TFBSs) to determine TFBS-association signatures that can be used for discriminating specific regulatory functions.
- DiRE's unique feature is its ability to detect REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search.
- DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function or other biologically meaningful grouping.
- The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs and it also scores the association of individual transcription factors (TFs) with the biological function shared by the group of input genes.
- Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.
Keywords:
- regulatory elements
- REs
- gene expression regulation
- enhancers
- repressors
- silencers
- enhance identification
- distant regulatory elements
- transcription factor binding sites
- TFBS
- regulatory function
Literature & Tutorials:
This record last updated: 07-21-2008