ChIP-chip Data

DNA-binding proteins

• Constitutive proteins (mostly histones)– Organize DNA– Regulate access to DNA– Have many modifications

• Acetylation, methylation, …

• Sporadic proteins (Transcription Factors)– Mediate docking of transcription apparatus– Modify histones– Methylate DNA

Histones

Histones are an ancient family of proteins which serve as the scaffold for DNA

Four types of histones assemble in pairs to form a nucleosome

DNA is wrapped twice around each nucleosome

Histones and Modifications

DNA contacts histones on their tails Histone tails can be modified

Histones can stay loose or assemble tightly – this compacts the DNA

Transcription Factors

• General – help to set up transcription of many genes

• Specific – draw in general factors or RNA Pol II to specific genes

TATABindingProtein

DNA Methylation

Adding a Methyl to Cytosine

Cytosine methylation is passed on to daughter cells

Chromatin Immuno-precipitation

Tiling Array

• One probe every n base pairs over some length of chromosome

– Interrupted by repeat regions

• Promoter array: each (known) promoter tiled

An Affymetrix tiling design

What the data look like

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histone acetylation on 15 samples over one promoter (raw)

Multiple Promoters

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Normalized by Medians

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Methods and Issues

• Normalization– Different enrichment ratios– Different probe thermodynamics– Dye and probe bias

• Estimation– Categorical or continuous?– Individual values are noisy:

• For TF binding: where is the peak?----

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Normalization

• Basic idea: compensate technical variables

• Technique differences should affect different probes differently

• Try to estimate what part of signal can be attributed to technical factors

• Easiest variable to access: sequence

• One color Affy array– Needs separate array for comparison

• Normalizes probe thermodynamics & enrichment ratio

• Estimation by (robust) moving average

Normalized Data – Rare Event

Normalized Data – Common Event

Estimation

• Try to build an intelligent moving average

• Not all neighbors will be similar

• Typical TF binds to 8bp– Pol II may spread wider

• Typical fragment is 100-200 bp

• Cannot resolve < 200 bp----

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Pol II binding on a 100 bp grid

TileMap

• Ignores normalization

• ‘Shrinkage’ estimator of variance– Improves individual scores

• Smooths noise by moving average

ChIP-chip Data

Documents

Transcript of ChIP-chip Data

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Synergy 2000 Chip Casanave President Data Access Corporation.

ChIP-seq data analysis...2018/11/07 · ChIP-seq data analysis Introduction to practicals II: diﬀerential binding & functional annotations

Exploring and Understanding ChIP-Seq data · Exploring and Understanding ChIP-Seq data Simon Andrews simon.andrews@babraham.ac.uk @simon_andrews v2020-05. Data Creation and Processing

Application of Gene Chip and Data Processing

ChIP-Seq Data Processing - Genes & Developmentgenesdev.cshlp.org/.../Supplemental_Materials.docx · Web viewshows ChIP-seq control experiments including inhibitor studies, validation

ChIP-chip: Data, Model, and Analysis - UCLA Statisticsywu/research/papers/biom_768.pdfChIP-chip: Data, Model, and Analysis 789 protein. The binding at diﬀerent binding sites is assumed

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Some Basic Analyis of ChIP-Seq Data - Bioconductormaster.bioconductor.org/.../ChIP-seq/workflow.pdf · 2008. 11. 18. · Some Basic Analyis of ChIP-Seq Data November 14, 2008 Our

On-Chip Antennas for Multi- Chip RF Data Transmission€¦ · On-Chip Antennas for Multi-Chip RF Data Transmission Dr. Kathleen Melde Professor, ECE University of Arizona Department

Analysis of ChIP-Seq Data

Exploiting Fine-Grained Data Parallelism with Chip ...meiyang/ecg700/readings/Exploiting Fine...Exploiting Fine-Grained Data Parallelism with Chip Multiprocessors and Fast Barriers

Data Acquisition System Basis Chip

20091110 Technical Seminar ChIP-seq Data Analysis

Hybrid On-chip Data Networks - Columbia Universitylightwave.ee.columbia.edu/files/Hendry2010b.pdf · Hybrid On-chip Data Networks ... Local Write Optical send Remote Read Electronic

ChIP-seq Data Analysis

MACHINING DATA COMPARISON - Kaiser Aluminum DATA COMPARISON Drill Chip Form Chip Turning Chip Alloy 6262 Alloy 6033 A technology-driven replacement for Alloys 6061 and 6262 with good

A Prototype Data Acquisition Chip for Large-area ...psec.uchicago.edu/Documents/thesis_vansanten.pdfA Prototype Data Acquisition Chip for Large-area, Picosecond Resolution, Time ...