Discovery of regulatory elements by a computational method for phylogenetic footprinting.
By M. Blanchette, Martin Tompa. Genome Research, 2002
359 citations recorded by the source corpus.
Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/59afc62e90eb540ecd408210b22262c1d406f5fc
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Modan K. Das
- Ho-Kwok Dai
- Manolis Kellis
- E. van Nimwegen
- Eric D. Siggia
- Rahul Siddharthan
- Eric S. Lander
- Ting Wang
In Plant Science
- Rasmus Nielsen
- Tal Pupko
- Modan K. Das
- Manolis Kellis
- Ho-Kwok Dai
- Eric S. Lander
- Peter Beerli
- MARK A. Beaumont
Citations in the corpus
- Sequencing and comparison of yeast species to identify genes and regulatory elements (2003, methodology): “This approach has long been used to study promoters of specific genes in many organisms 11,13,24,38,39 , and recently was applied across the entire human and mouse genomes 7 .”
- Comparative Genomics in Eukaryotes (2005, neutral): “Phylogenetic footprinting (Blanchette and Tompa, 2002) is the method that finds conserved sequences of DNA between upstream regions of orthologous genes and is named after its experimental equivalent to find the location of binding of regulatory proteins.”
- A survey of DNA motif finding algorithms (2007, methodology): “However, it has been observed [3,4,62] that this approach to phylogenetic foot-printing does not always work.”
- Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. (2006, background): “Therefore, highly conserved sequences in a collection of homologous regions are good candidates for functioning as regulatory elements (Blanchette and Tompa, 2002).”
- Molecular signatures of natural selection. (2005, background): “Inferences regarding selection have therefore been used extensively to identify functional regions or protein residues ( 12 , 91).”
- Combining phylogenetic data with co-regulated genes to identify regulatory motifs (2003, background): “Over the past few years, several algorithms have been developed for this purpose, including Gibbs sampler (Lawrence et al ., 1993), Consensus (Stormo and Hartzell, 1989; Hertz and Stormo, 1999), MEME (Bailey and Elkan, 1994, 1995), ANN-Spec (Workman and Stormo, 2000), AlignACE (Hughes et al ., 2000)”
- PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny (2005, background): “Focusing only on the conserved blocks, as is done in phylogenetic footprinting approaches [13–17], misses a significant fraction of true regulatory sites, and we thus chose to include all sequence.”