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Identifying ChIP-seq enrichment using MACS
- Jianxing Feng, T. Liu, Bo Qin, Yong Zhang, Xiaole Shirley Liu
- Computer ScienceNature Protocols
- 1 September 2012
This protocol provides a detailed demonstration of how to install MACS and how to use it to analyze three common types of ChIP-seq data sets with different characteristics: the sequence-specific transcription factor FoxA1, the histone modification mark H3K4me3 with sharp enrichment and theH3K36me3 mark with broad enrichment.
Cistrome: an integrative platform for transcriptional regulation studies
A web-based application called Cistrome, based on the Galaxy open source framework, that has 29 ChIP-chip- and Chip-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery.
Differential chromatin marking of introns and expressed exons by H3K36me3
- P. Kolasinska-Zwierz, T. Down, I. Latorre, T. Liu, X. Liu, J. Ahringer
- BiologyNature Genetics
- 22 December 2008
It is proposed that H3K36me3 exon marking in chromatin provides a dynamic link between transcription and splicing, and is found at lower levels in alternatively spliced exons, supporting a splicing-related marking mechanism.
Broad chromosomal domains of histone modification patterns in C. elegans.
The genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae are defined, allowing for in-depth analysis of the organization and deployment of the C. elegans genome during development.
Using MACS to Identify Peaks from ChIP‐Seq Data
This unit describes two basic protocols that provide detailed information on how to use MACS to identify either the binding sites of a transcription factor or the enriched regions of a histone modification with broad peaks.
Identification of Conversion from Mild Cognitive Impairment to Alzheimer's Disease Using Multivariate Predictors
This study establishes meaningful multivariate predictors composed of selected NM, MRI and CSF measures which may be useful and practical for clinical diagnosis.
A Meta-Analysis of Oxidative Stress Markers in Depression
A meta-analysis supports the facts that the serum TAC, paraoxonase and antioxidant levels are lower, and the serum free radical and oxidative damage product levels are higher than controls in depressed patients, while the antioxidants levels are increased and the oxidative damage products levels are decreased after antidepressant medication.
Establishing the Proteome of Normal Human Cerebrospinal Fluid
This normal CSF proteome establishes a comparative standard and basis for investigations into a variety of diseases with neurological and psychiatric features and represents the most comprehensive characterization of truenormal CSF to date.
Lynch syndrome (hereditary nonpolyposis colorectal cancer) diagnostics.
- Kristina Lagerstedt Robinson, T. Liu, A. Lindblom
- MedicineJournal of the National Cancer Institute
- 21 February 2007
The findings suggest that missense MMR gene mutations are common in HNPCC and that germline MMR mutations are also found in patients with MSI-negative tumors.
Systematic evaluation of factors influencing ChIP-seq fidelity
Evaluation of widely used ChIP-seq analysis tools suggests that adjustments or algorithm improvements are required to handle data sets with deep coverage, and a chromatin-state bias was detected: open chromatin regions yielded higher coverage, which led to false positives if not corrected.