Unsupervised Classification for Tiling Arrays: ChIP-chip and Transcriptome
نویسندگان
چکیده
منابع مشابه
Unsupervised classification for tiling arrays: ChIP-chip and transcriptome.
Tiling arrays make possible a large-scale exploration of the genome thanks to probes which cover the whole genome with very high density, up to 2,000,000 probes. Biological questions usually addressed are either the expression difference between two conditions or the detection of transcribed regions. In this work, we propose to consider both questions simultaneously as an unsupervised classific...
متن کاملModel-based analysis of tiling-arrays for ChIP-chip.
We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model,...
متن کاملStarr: Simple Tiling ARRay analysis for Affymetrix ChIP-chip data
Starr is an extension of the Ringo [6] package for the analysis of ChIP-chip projects. Whereas the latter is specialized to the processing of Nimblegen and Agilent arrays, the former provides all corresponding features for Affymetrix arrays. Data can be read in from Affymetrix CEL-files, or from text files in gff format. Standard quality assessment and data normalization tools are available. St...
متن کاملNTAP: for NimbleGen tiling array ChIP-chip data analysis
SUMMARY NTAP is designed to analyze ChIP-chip data generated by the NimbleGen tiling array platform and to accomplish various pattern recognition tasks that are useful especially for epigenetic studies. The modular design of NTAP makes the data processing highly customizable. Users can either use NTAP to perform the full process of NimbleGen tiling array data analysis, or choose post-processing...
متن کاملA hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences
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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ژورنال
عنوان ژورنال: Statistical Applications in Genetics and Molecular Biology
سال: 2011
ISSN: 1544-6115,2194-6302
DOI: 10.2202/1544-6115.1692