Computational methodology for ChIP-seq analysis
نویسندگان
چکیده
منابع مشابه
Computational analysis of ChIP-seq data.
Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology to map protein-DNA interactions in a genome. The genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics of ChIP-seq data and introduces a computat...
متن کاملEpigenetic analysis: ChIP-chip and ChIP-seq.
The access of transcription factors and the replication machinery to DNA is regulated by the epigenetic state of chromatin. In eukaryotes, this complex layer of regulatory processes includes the direct methylation of DNA, as well as covalent modifications to histones. Using next-generation sequencers, it is now possible to obtain profiles of epigenetic modifications across a genome using chroma...
متن کاملDifferential principal component analysis of ChIP-seq.
We propose differential principal component analysis (dPCA) for analyzing multiple ChIP-sequencing datasets to identify differential protein-DNA interactions between two biological conditions. dPCA integrates unsupervised pattern discovery, dimension reduction, and statistical inference into a single framework. It uses a small number of principal components to summarize concisely the major mult...
متن کاملExPlainTM Analysis of TAL1 ChIP-seq Intervals
Next generation sequencing (NGS) technologies have opened up novel research possibilities in many areas including cancer research, gene regulation, epigenetics, personalized medicine and pharmacogenomics. ChIP-seq is a remarkable NGS-based approach to uncover functional features of the DNA on a genome-wide scale and in great detail. A major application area of ChIP-seq is the discovery of trans...
متن کاملA comprehensive comparison of tools for differential ChIP-seq analysis
ChIP-seq has become a widely adopted genomic assay in recent years to determine binding sites for transcription factors or enrichments for specific histone modifications. Beside detection of enriched or bound regions, an important question is to determine differences between conditions. While this is a common analysis for gene expression, for which a large number of computational approaches hav...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Quantitative Biology
سال: 2013
ISSN: 2095-4689,2095-4697
DOI: 10.1007/s40484-013-0006-2