Predicting rules on organization of cis-regulatory elements, taking the order of elements into account

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Predicting rules on organization of cis-regulatory elements, taking the order of elements into account

MOTIVATION In eukaryotes, rules regarding organization of cis-regulatory elements are complex. They sometimes govern multiple kinds of elements and positional restrictions on elements. RESULTS We propose a method for detecting rules, by which the order of elements is restricted. The order restriction is expressed as element patterns. We extract all the element patterns that occur in promoter ...

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Transposable elements (TEs) are mobile genetic sequences that can jump around the genome from one location to another, behaving as genomic parasites. TEs have been particularly effective in colonizing mammalian genomes, and such heavy TE load is expected to have conditioned genome evolution. Indeed, studies conducted both at the gene and genome levels have uncovered TE insertions that seem to h...

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Coevolutionary networks of splicing cis-regulatory elements.

Accurate and efficient splicing of eukaryotic pre-mRNAs requires recognition by trans-acting factors of a complex array of cis-acting RNA elements. Here, we developed a generalized Bayesian network to model the coevolution of splicing cis elements in diverse eukaryotic taxa. Cross-exon but not cross-intron compensatory interactions between the 5' splice site (5'ss) and 3' splice site (3'ss) wer...

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Recognition of cis-Regulatory Elements with Vombat

Variable order Markov models and variable order Bayesian trees have been proposed for the recognition of cis-regulatory elements, and it has been demonstrated that they outperform traditional models such as position weight matrices, Markov models, and Bayesian trees for the recognition of binding sites in prokaryotes. Here, we study to which degree variable order models can improve the recognit...

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It is now established that, as compared to normal cells, the cancer cell genome has an overall inverse distribution of DNA methylation ("methylome"), i.e., predominant hypomethylation and localized hypermethylation, within "CpG islands" (CGIs). Moreover, although cancer cells have reduced methylation "fidelity" and genomic instability, accurate maintenance of aberrant methylomes that underlie m...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2004

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/bth049