Name: a novel bayesian change-point algorithm for genome-wide analysis of diverse chipseq data types
Uploaded: 2012-12-10T12:00:00
Description: Watch this Scientific Journal Video about A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types at JoVE.com

斯塔尔基金会奖（MQZ），美国国立卫生研究院授予ES017166（MQZ），美国国家科学基金会：授予DMS0906593（HX）。

1。准备输入文件BCP分析<ol><li>对齐短期运行（芯片和输入库）使用首选短读校准软件到相应的参考基因组测序读。映射的位置应该被转换为6列浏览器的可扩展的数据格式（BED）13（UCSC基因组浏览器， <a href="http://genome.ucsc.edu/" target="_blank">http://genome.ucsc.edu/</a> ），制表符分隔的每行对应的读表示映射的染色体，起始位置（从0开始），结束位置（半开），读的名字，得分（可选）和链。 <...

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我们的目标是建立一个模型分析ChIPseq数据同样可以识别点状和弥漫性两种数据结构。到现在为止，富集的地区，尤其是弥漫性的地区，这反映了先决条件预期的大岛，大小，已经难以辨认。为了解决这些问题，我们利用最新进展在HMM的技术，具有许多优点，现有的的的启发式模型和缺乏创新的HMM模型。 我们的模型使用明确的公式与贝叶斯框架。从其他HMM模型，这是一个关键?...

<table border="1"><tbody><tr><td> 的试剂的名称 </td><td> 公司 </td><td> 目录编号 </td><td> 评论（可选） </td></tr><tr><td>基于Linux的工作站</td><td></td><td></td><td></td></tr></tbody></table>

a novel bayesian change-point algorithm for genome-wide analysis of diverse chipseq data types

ChIPseq是一种广泛使用的技术，用于调查蛋白质-DNA相互作用。读密度分布所产生的使用下一个 - 蛋白结合的DNA测序和对准读取到参考基因组的短。富集的区域显示峰，这往往显着不同的形状，这取决于对目标蛋白1。例如，转录因子通常在现场和序列特异性方式结合，往往会产生点状的山峰，而组蛋白修饰更普遍的特点是广泛的，弥漫性的岛屿富集2。可靠地识别这些地区是我们的工作重点。 算法分析ChIPseq数据采用各种方法，启发式3-5进行更加严格的统计模型， 例如隐马尔可夫模型（HMM模型）6-8。我们试图最小化的必要性难以界定，专案参数，通常的解决方案，妥协的分辨率和减轻直观的工具的可用性。基于HMM的方法，我们的目的是限制参数估计的程序和简单的，有限状态分类，往往利用。 此外，传统ChIPseq的数据分析包括分类的读取密度分布为点状或弥漫性的后续应用适当的工具。我们还旨在取代这两个不同的模型需要一个单一的，更灵活的模型，它可以足够能力解决整个频谱的数据类型。 为了实现这些目标，我们首先构建了一个统计框架，自然为蓝本ChIPseq数据结构尖端提前HMM模型9，利用唯一明确的公式，其性能优势的关键创新。更复杂的启发式模型，通过我们的的HMM可容纳无限的隐藏状态贝叶斯模型。我们把它应用在读取密度，进一步定义丰富的段，确定合理的变化点。我们的分析表明，我们的贝叶斯变点（BCP）算法具有降低计算复杂度，证明了一个简化的运行时间和内存占用。 BCP算法已成功地应用于斑点状的峰值和漫岛的识别与强​​大的精度和有限的用户定义的参数。这所示，它的多功能性和易用性。因此，我们认为它可以容易地实现在广泛的范围内的数据类型和最终用户的方式，很容易比较和对比，使其成为一个伟大的工具ChIPseq数据的分析，可以帮助研究团体之间的协作和佐证。在这里，我们演示了应用程序的BCP现有的转录因子10,11和表观数据来说明它的用处。

BCP擅长识别组蛋白修饰数据的广泛富集的地区。作为一个参照点，我们以前相比，我们的研究结果的SICER 3，现有的工具，已显示出强大的性能。为了更好地说明BCP的优势，我们研究了组蛋白的修饰，得到了很好的研究，建立评估成功率的基础。然后考虑到这一点，我们分析H3K36me3，因为它已经显示出强烈的积极转录基因体（ 图1）关联。相反，H3K36me3也被证明是互斥H3K27me3压?...

Watch this Scientific Journal Video about A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types at JoVE.com

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

我们的贝叶斯变点（BCP）算法的基础上通过隐马尔可夫模型的造型变化点的国家的最先进的进步和应用染色质免疫沉淀测序（ChIPseq）数据分析。 BCP执行在广泛和点状数据类型，但擅长准确地识别健壮的，可重复的岛屿弥漫组蛋白富集。

一种新型的全基因组分析的贝叶斯变点算法的多元ChIPseq数据类型

ChIPseq is a widely used technique for investigating protein-DNA interactions. Read density profiles are generated by using next-sequencing of ...

Research

JoVE Journal

Biology

Genome-wide Analysis of Aminoacylation (Charging) Levels of tRNA Using Microarrays

Genome-wide Analysis of Aminoacylation Charging Levels of tRNA Using Microarrays

（充电）酰化tRNA的使用微阵列技术水平的全基因组分析

tRNA aminoacylation, or charging, levels can rapidly change within a cell in response to the environment[1]. Changes in tRNA charging levels in both ...

科研

生物学

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

采用芯片识别亚型特定的靶基因的全基因组分析

Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the ...

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

miRNA的目标使用的任务目标ID库的全基因组屏幕

The Target ID Library is designed to assist in discovery and identification of microRNA (miRNA) targets. The Target ID Library is a plasmid-based, ...

Two Types of Assays for Detecting Frog Sperm Chemoattraction

两种类型的检测，检测青蛙精子Chemoattraction

Sperm chemoattraction in invertebrates can be sufficiently robust that one can place a pipette containing the attractive peptide into a sperm suspension ...

Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

定量和自动化高通量的全基因组RNAi屏幕 C。线虫</em

RNA interference is a powerful method to understand gene function, especially when conducted at a whole-genome scale and in a quantitative context. In C. ...

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

全基因组基因缺失<em&gt;链球菌血统</em通过高通量PCR

Transposon  mutagenesis and single-gene deletion are two methods applied in genome-wide  gene knockout in bacteria 1,2. Although transposon mutagenesis is ...

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

多聚核糖体分离和哺乳动物Translatomes分析在基因组范围内

mRNA translation plays a central role in the regulation of gene expression and represents the most energy consuming process in mammalian cells. ...

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin

药物与DNA相互作用的细胞全基因组映射与COSMIC（小分子交联，染色质隔离）

The genome is the target of some of the most effective chemotherapeutics, but most of these drugs lack DNA sequence specificity, which leads to ...

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

从真核细胞染色体外的环状DNA基因组范围内的净化

Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs ...

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

葡萄全基因组鉴定与表达的综合工作流 E3 泛素连接基因家族的 Meta 分析

Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the ...