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

स्टार फाउंडेशन (MQZ) पुरस्कार, NIH अनुदान (MQZ) ES017166, NSF अनुदान DMS0906593 (सेमी).

1. BCP विश्लेषण के लिए इनपुट फाइल की तैयारी <ol><li> पढ़ता कम उपयुक्त संदर्भ पसंदीदा कम पढ़ा संरेखण सॉफ्टवेयर का उपयोग कर जीनोम रन (चिप और इनपुट पुस्तकालयों) अनुक्रमण से उत्पादित संरेखित करें. मैप किए गए स्थान...

<ol>
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हम बाहर सेट के लिए कि दोनों कबरा और फैलाना डेटा संरचनाओं को समान रूप से अच्छी तरह से पहचान सकता है ChIPseq डेटा का विश्लेषण करने के लिए एक मॉडल का विकास. अब तक, संवर्धन के क्षेत्रों, विशेष रूप से फैलाना क्षेत्?...

<table border="1"><tbody><tr><td> अभिकर्मक के नाम </td><td> कंपनी </td><td> सूचीपत्र संख्या </td><td> टिप्पणियां (वैकल्पिक) </td></tr><tr><td> लिनक्स आधारित वर्कस्टेशन </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 is a widely used technique for investigating protein-DNA interactions. Read density profiles are generated by using next-sequencing of protein-bound DNA and aligning the short reads to a reference genome. Enriched regions are revealed as peaks, which often differ dramatically in shape, depending on the target protein1. For example, transcription factors often bind in a site- and sequence-specific manner and tend to produce punctate peaks, while histone modifications are more pervasive and are characterized by broad, diffuse islands of enrichment2. Reliably identifying these regions was the focus of our work.
Algorithms for analyzing ChIPseq data have employed various methodologies, from heuristics3-5 to more rigorous statistical models, e.g. Hidden Markov Models (HMMs)6-8. We sought a solution that minimized the necessity for difficult-to-define, ad hoc parameters that often compromise resolution and lessen the intuitive usability of the tool. With respect to HMM-based methods, we aimed to curtail parameter estimation procedures and simple, finite state classifications that are often utilized.
Additionally, conventional ChIPseq data analysis involves categorization of the expected read density profiles as either punctate or diffuse followed by subsequent application of the appropriate tool. We further aimed to replace the need for these two distinct models with a single, more versatile model, which can capably address the entire spectrum of data types.
To meet these objectives, we first constructed a statistical framework that naturally modeled ChIPseq data structures using a cutting edge advance in HMMs9, which utilizes only explicit formulas-an innovation crucial to its performance advantages. More sophisticated then heuristic models, our HMM accommodates infinite hidden states through a Bayesian model. We applied it to identifying reasonable change points in read density, which further define segments of enrichment. Our analysis revealed how our Bayesian Change Point (BCP) algorithm had a reduced computational complexity-evidenced by an abridged run time and memory footprint. The BCP algorithm was successfully applied to both punctate peak and diffuse island identification with robust accuracy and limited user-defined parameters. This illustrated both its versatility and ease of use. Consequently, we believe it can be implemented readily across broad ranges of data types and end users in a manner that is easily compared and contrasted, making it a great tool for ChIPseq data analysis that can aid in collaboration and corroboration between research groups. Here, we demonstrate the application of BCP to existing transcription factor10,11 and epigenetic data12 to illustrate its usefulness.

BCP histone संशोधन डेटा में व्यापक संवर्धन के क्षेत्रों की पहचान करने में excels. संदर्भ का एक बिंदु के रूप में, हम पहले SICER 3, एक मौजूदा उपकरण है जो मजबूत प्रदर्शन का प्रदर्शन किया है उन लोगों के लिए हमारे परिणाम?...

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

हमारे Bayesian बदलें प्वाइंट (BCP) एल्गोरिथ्म हिडन मार्कोव मॉडल के माध्यम से मॉडलिंग परिवर्तन अंक में राज्य के कला अग्रिम पर बनाता है और उन्हें chromatin immunoprecipitation (ChIPseq) डेटा विश्लेषण अनुक्रमण के लिए लागू होता है. BCP दोनों व्यापक और कबरा डेटा प्रकार में अच्छी तरह से करता है, लेकिन सही फैलाना histone संवर्धन के मजबूत, प्रतिलिपि प्रस्तुत करने योग्य द्वीपों की पहचान करने में excels.

विविध ChIPseq डेटा प्रकार के एक उपन्यास Bayesian बदलें बिंदु जीनोम चौड़ा विश्लेषण के लिए एल्गोरिथ्म

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

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