منابع مشابه
Predicting transcription factor synergism.
Transcriptional regulation is mediated by a battery of transcription factor (TF) proteins, that form complexes involving protein-protein and protein-DNA interactions. Individual TFs bind to their cognate cis-elements or transcription factor-binding sites (TFBS). TFBS are organized on the DNA proximal to the gene in groups confined to a few hundred base pair regions. These groups are referred to...
متن کاملInvestigating transcription factor synergism in humans
Proteins are the core and the engine of every process in cells thus the study of mechanisms that drive the regulation of protein expression, is essential. Transcription factors play a central role in this extremely complex task and they synergically co-operate in order to provide a fine tuning of protein expressions. In the present study, we designed a mathematically well-founded procedure to i...
متن کاملPredicting transcription factor specificity with all-atom models Citation
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rath...
متن کاملAssessing phylogenetic motif models for predicting transcription factor binding sites
MOTIVATION A variety of algorithms have been developed to predict transcription factor binding sites (TFBSs) within the genome by exploiting the evolutionary information implicit in multiple alignments of the genomes of related species. One such approach uses an extension of the standard position-specific motif model that incorporates phylogenetic information via a phylogenetic tree and a model...
متن کاملPredicting transcription factor affinities to DNA from a biophysical model
MOTIVATION Theoretical efforts to understand the regulation of gene expression are traditionally centered around the identification of transcription factor binding sites at specific DNA positions. More recently these efforts have been supplemented by experimental data for relative binding affinities of proteins to longer intergenic sequences. The question arises to what extent these two approac...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2002
ISSN: 1362-4962
DOI: 10.1093/nar/gkf535