SimBindProfiles: Similar Binding Profiles, identifies common and unique regions in array genome tiling array data
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Optimized design and assessment of whole genome tiling arrays
MOTIVATION Recent advances in microarray technologies have made it feasible to interrogate whole genomes with tiling arrays and this technique is rapidly becoming one of the most important high-throughput functional genomics assays. For large mammalian genomes, analyzing oligonucleotide tiling array data is complicated by the presence of non-unique sequences on the array, which increases the ov...
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Microarrays have been developed that tile the entire nonrepetitive genomes of many different organisms, allowing for the unbiased mapping of active transcription regions or protein binding sites across the entire genome. These tiling array experiments produce massive correlated data sets that have many experimental artifacts, presenting many challenges to researchers that require innovative ana...
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MOTIVATION Transcription factors (TFs) regulate gene expression by recognizing and binding to specific regulatory regions on the genome, which in higher eukaryotes can occur far away from the regulated genes. Recently, Affymetrix developed the high-density oligonucleotide arrays that tile all the non-repetitive sequences of the human genome at 35 bp resolution. This new array platform allows fo...
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With high throughput experiments like tiling array and NGS, researchers are looking for continuous homogeneous segments or signal peaks, which would represent chromatin states, methylation ratio, transcripts or genome regions of deletion and amplification. While in a normal experimental set-up, these profiles would be generated for multiple samples or conditions with replicates. In the package ...
متن کاملStatistical Applications in Genetics and Molecular Biology
High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-v...
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تاریخ انتشار 2013