.png){kind=icon}
返回
An integrated software system for analyzing ChIP-chip and ChIP-seq data
.png){kind=icon}
OA
AI
DOI：10.1038/nbt.1505.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (hIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP-microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information. We demonstrate the use of these tools by a comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis with or without a negative control sample, and an analysis of a new motif in Nanog- and Sox2-binding regions.
Keyword:
EMBRYONIC STEM-CELLS
TRANSCRIPTIONAL REGULATORY CIRCUITRY
FACTOR-BINDING SITES
GENOME-WIDE ANALYSIS
MODEL-BASED ANALYSIS
CHROMATIN-IMMUNOPRECIPITATION
IN-VIVO
DNA-BINDING
PROTEIN
ARRAYS
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
IF:
41.7
论文数:
1.2W
被引数:
10.1W
机构
引用论文
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes脊椎动物，昆虫，蠕虫和酵母基因组中的进化保守元素.png)
GENOME RESEARCH
OAAI
GENOME RESEARCHIF5.5
OAAI分享收藏分享收藏TRANSFAC® and its module TRANSCompel®:: transcriptional gene regulation in eukaryotesTRANSFAC®及其模块TRANSCompel®:: 真核生物中的转录基因调控NUCLEIC ACIDS RESEARCHOAAI
NUCLEIC ACIDS RESEARCHIF13.1
OAAI分享收藏
查看更多内容