Genes associated with the cis-regulatory functions of intragenic LINE-1 elements
نویسندگان
چکیده
منابع مشابه
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.
AlignACE is a Gibbs sampling algorithm for identifying motifs that are over-represented in a set of DNA sequences. When used to search upstream of apparently coregulated genes, AlignACE finds motifs that often correspond to the DNA binding preferences of transcription factors. We previously used AlignACE to analyze whole genome mRNA expression data. Here, we present a more detailed study of its...
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BACKGROUND Cryptosporidiosis is a ubiquitous infectious disease, caused by the protozoan parasites Cryptosporidium hominis and C. parvum, leading to acute, persistent and chronic diarrhea worldwide. Although the complications of this disease can be serious, even fatal, in immunocompromised patients of any age, they have also been found to lead to long term effects, including growth inhibition a...
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We present a computational pipeline to predict cis-regulatory elements composing results based on different algorithms: Clover, Cluster-Buster, an own implementation of human/rat/mouse sequence identity and our ITB algorithm. The procedure uses information from the human genome sequence, NCBI gene annotations, verified eukaryotic promoters (EPD), experimentally proven binding sites (Transfac) a...
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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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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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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2013
ISSN: 1471-2164
DOI: 10.1186/1471-2164-14-205