Signal search analysis: a new method to localize and characterize functionally important DNA sequences
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Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction tools, we have begun a systematic study of the sequence-sp ...
A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcript ...
Fibrates have been reported to modulate plasma high density lipoprotein cholesterol and apolipoprotein (apo) A-I concentrations. Therefore, the molecular mechanisms underlying the regulation of human apoA-I gene expression by fibrates was investigated. Fen ...
The ability to determine the location and relative strength of all transcription-factor binding sites in a genome is important both for a comprehensive understanding of gene regulation and for effective promoter engineering in biotechnological applications ...
An emerging model views gene regulation as a competition for regulatory sequences between transcription factors and nucleosomes at thermodynamic equilibrium. A computational model of the DNA affinity of nucleosomes was recently developed allowing to predic ...
The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in th ...
Heritable changes to the transcriptome that are independent to changes in the genome are defined as epigenetics. DNA methylation and posttranslational modifications of histones, such as acetylation/deacetylation and methylation/demethylation of lysine resi ...
Since the advent of microarrays, vast amounts of gene expression data have been generated. However, these microarray data fail to reveal the transcription regulatory mechanisms that underlie differential gene expression, because the identity of the respons ...
"There is more virus in us than us in us". John Coffin's famous sentence illustrates that particular nucleic acid sequences related to exogenous viruses, called retrotransposons, constitute almost half of the human genome and largely exceeds the amount of ...
The sequencing of the human genome revealed that the C2H2-zinc finger proteins (ZFPs) are the largest family of human transcription factors. Around 300 members of this family contain, in addition to their zinc finger motifs, a KRAB domain that has been imp ...