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MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets.

Genome biology | Mar 16, 2012

ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed. Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.

Pubmed ID: 22424423 RIS Download

Mesh terms: Algorithms | Binding Sites | Chromatin | Chromatin Immunoprecipitation | Embryonic Stem Cells | Epigenesis, Genetic | Gene Expression Profiling | Genome, Human | Genome-Wide Association Study | Genomics | HeLa Cells | Histones | Humans | K562 Cells | Models, Genetic | Organ Specificity | Protein Binding | Transcription Factors

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UCSC Genome Browser

A collection of genomes which include reference sequences and working draft assemblies, as well as a variety of tools to explore these sequences. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets. Also provided is a portal to the Encyclopedia of DNA Elements (ENCODE) and Neandertal projects.

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