Assessing Computational Methods of Cis-Regulatory Module Prediction
نویسندگان
چکیده
منابع مشابه
Assessing Computational Methods of Cis-Regulatory Module Prediction
Computational methods attempting to identify instances of cis-regulatory modules (CRMs) in the genome face a challenging problem of searching for potentially interacting transcription factor binding sites while knowledge of the specific interactions involved remains limited. Without a comprehensive comparison of their performance, the reliability and accuracy of these tools remains unclear. Fac...
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Lack of knowledge about how regulatory regions evolve in relation to their structure-function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic cis-regulatory module-the even-skipped stripe 2 enhancer-from four Drosophila species. T...
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∆u = ∂2u ∂x1 + ∂2u ∂x2 where x = (x1, x2) ∈ IR 2 are Cartesian coordinates. Even though the Poisson equation looks very special it is an important model case representing several problems from physics based on energy minimisation. Variations of the techniques we will study apply to a wide class of second order so-called elliptic problems. It is known that there are cases where no classical (i.e...
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MOTIVATION The transcriptional regulation of a metazoan gene depends on the cooperative action of multiple transcription factors that bind to cis-regulatory modules (CRMs) located in the neighborhood of the gene. By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription. RESULTS Based on the hypothesis that genes that are needed in exactly th...
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Eukaryotic gene control regions are known to be spread throughout non-coding DNA sequences which may appear distant from the gene promoter. Transcription factors are proteins that coordinately bind to these regions at transcription factor binding sites to regulate gene expression. Several tools allow to detect significant co-occurrences of closely located binding sites (cis-regulatory modules, ...
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ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2010
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1001020