ChIP-chip Data

18
ChIP-chip Data

TAGS:

description

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. - PowerPoint PPT Presentation

Transcript of ChIP-chip Data

Page 1: ChIP-chip Data

ChIP-chip Data

Page 2: 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

Page 3: ChIP-chip Data

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

Page 4: ChIP-chip Data

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

Page 5: ChIP-chip Data

Transcription Factors

• General – help to set up transcription of many genes

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

TATABindingProtein

Page 6: ChIP-chip Data

DNA Methylation

Adding a Methyl to Cytosine

Cytosine methylation is passed on to daughter cells

Page 7: ChIP-chip Data

Chromatin Immuno-precipitation

Page 8: ChIP-chip Data

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

Page 9: ChIP-chip Data

What the data look like

__ _

_

__ _ __

_

_____

1206600 1206800 1207000 1207200 1207400

-2-1

01

23

4

loc[nn]

lr(e

co

g1

.h3

k9

)[n

n, ]

_

__

_

_ _ _ ___ _____

__ _

_

_ __

___ ___

__

__

__

__

____

_____

__

_ _

_ __

___

____

_

_

_

_

_

_ _ _ ___

_

____

__

_

_

_ __

____

___

_

__

_ _

_ _

__

__ _

__

__

___

_

__

_ ___ _

_

___

__ _

_

_

__ ___

_

____

___

_

__ _

___

_

___

_

__

_ _

_ _

_

_

_

_

_

_

___

__ _

_

_ _

_ ____

_

___

__ __

_ _ _

___ _

____

histone acetylation on 15 samples over one promoter (raw)

Page 10: ChIP-chip Data

Multiple Promoters

----

--

--

----

-------------

--------

-

-

-

- ---

--

--

-

-

-

------------- -

-

------------------

---------

---

10120000 10125000 10130000 10135000

-4-3

-2-1

01

2

loc[mm]

log

.R[m

m, ] -

log

.G[m

m, ]

---

-

------

-

------

---------

-----------

-----

--------

---------- --

---

-------

-----------------

- -

-

-

----

-

--

--

---

-

-

---------------------- --------

------

---

------

-- -

--

-------

--

--

----

--------

--

--

-

-------

--

-

-

-

--

---

-

-

------------

-

-

-

----

--

-

--

-----

-

-

----

-

---

-

-

----

----

---

---

-

-

-

--

-

-

-

--

-----

--

Page 11: ChIP-chip Data

Normalized by Medians

----

--

--

----

---------

----

---

---

--

-

-

-

- ---

--

--

-

-

-

------

---

---- -

-

------------------

-----

----

---

10120000 10125000 10130000 10135000

-2-1

01

23

loc[mm]

xx

---

-

------

-

-----

-

---------

----------

---

---

------------------ --

---

-------

----

-------------- -

--

---

-

-

--

--

---

-

-

---------------------- --------

------

---

------

-

- -

--

-------

--

--

----

--------

--

--

-

-

------

--

-

-

-

--

---

-

-

------------

-

-

-

----

--

-

--

-----

-

-

----

-

---

-

-

----

----

---

---

-

-

-

--

-

-

-

--

-----

--

Page 12: ChIP-chip Data

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?----

--

--

----

---------

----

---

---

--

-

-

-

- ---

--

--

-

-

-

------

---

---- -

-

------------------

-----

----

---

10120000 10125000 10130000 10135000

-2-1

01

23

loc[mm]

xx

---

-

------

-

-----

-

---------

----------

---

---

------------------ --

---

-------

----

-------------- -

--

---

-

-

--

--

---

-

-

---------------------- --------

------

---

------

-

- -

--

-------

--

--

----

--------

--

--

-

-

------

--

-

-

-

--

---

-

-

------------

-

-

-

----

--

-

--

-----

-

-

----

-

---

-

-

----

----

---

---

-

-

-

--

-

-

-

--

-----

--

Page 13: ChIP-chip Data

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

Page 14: ChIP-chip Data

MAT

• One color Affy array– Needs separate array for comparison

• Normalizes probe thermodynamics & enrichment ratio

• Estimation by (robust) moving average

Page 15: ChIP-chip Data

Normalized Data – Rare Event

Page 16: ChIP-chip Data

Normalized Data – Common Event

Page 17: ChIP-chip Data

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----

--

--

----

---------

----

---

---

--

-

-

-

- ---

--

--

-

-

-

------

---

---- -

-

------------------

-----

----

---

10120000 10125000 10130000 10135000

-2-1

01

23

loc[mm]

xx

---

-

------

-

-----

-

---------

----------

---

---

------------------ --

---

-------

----

-------------- -

--

---

-

-

--

--

---

-

-

---------------------- --------

------

---

------

-

- -

--

-------

--

--

----

--------

--

--

-

-

------

--

-

-

-

--

---

-

-

------------

-

-

-

----

--

-

--

-----

-

-

----

-

---

-

-

----

----

---

---

-

-

-

--

-

-

-

--

-----

--

Pol II binding on a 100 bp grid

Page 18: ChIP-chip Data

TileMap

• Ignores normalization

• ‘Shrinkage’ estimator of variance– Improves individual scores

• Smooths noise by moving average


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

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

Data Criticality in Network-On-Chip Design...Data Criticality in Network-On-Chip Design Joshua San Miguel Natalie Enright Jerger Network-On-Chip Efficiency 2 Efficiency is the ability

Data Criticality in Network-On-Chip Design...Data Criticality in Network-On-Chip Design Joshua San Miguel Natalie Enright Jerger Network-On-Chip Efficiency 2 Efficiency is the ability

Bell 202 chip data sheet

Bell 202 chip data sheet

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

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

ChIP-seq - Data processing

ChIP-seq - Data processing

Características del Chip / Chip Data Sheet ...jisoiluminacion.es/FichasTecnicas/FT51022.pdf · Caractéristiques de la Luminaire Ficha Técnica / Data Sheet / Fiche Technique Ref.

Características del Chip / Chip Data Sheet ...jisoiluminacion.es/FichasTecnicas/FT51022.pdf · Caractéristiques de la Luminaire Ficha Técnica / Data Sheet / Fiche Technique Ref.

Pic16f877a Data Chip

Pic16f877a Data Chip

SYN6288ChineseSpeech synthesis chip Data Sheet

SYN6288ChineseSpeech synthesis chip Data Sheet

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

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

Application of Gene Chip and Data Processing

Application of Gene Chip and Data Processing

Chip arrays and gene expression data. Motivation.

Chip arrays and gene expression data. Motivation.

Data Criticality in Network-On-Chip Design

Data Criticality in Network-On-Chip Design

ChIP Capture Sequencing (ChIP-CapSeq): A …Sequencing Application Note • 2016 3 Figure 3: Comparison of ChIP-Seq and ChIP-CapSeq data. A. RUNX1 locus. B. BACH1 locus. C. USP25 locus.

ChIP Capture Sequencing (ChIP-CapSeq): A …Sequencing Application Note • 2016 3 Figure 3: Comparison of ChIP-Seq and ChIP-CapSeq data. A. RUNX1 locus. B. BACH1 locus. C. USP25 locus.

20091110 Technical Seminar ChIP-seq Data Analysis

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

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

Analysis of ChIP-Seq Data

Analysis of ChIP-Seq Data

Practical - ChIP-seq data analysis - University of Helsinki · Practical - ChIP-seq data analysis Borbala Gerle European Bioinformatics Institute, Cambridge, UK Kathi Zarnack University

Practical - ChIP-seq data analysis - University of Helsinki · Practical - ChIP-seq data analysis Borbala Gerle European Bioinformatics Institute, Cambridge, UK Kathi Zarnack University

Supplementary Methods ChIP-chip and data analysisgenesdev.cshlp.org/content/suppl/2010/01/15/gad.1882610.DC1/WangSuppMat.pdfSupplementary Methods ChIP-chip and data analysis Chromatin

Supplementary Methods ChIP-chip and data analysisgenesdev.cshlp.org/content/suppl/2010/01/15/gad.1882610.DC1/WangSuppMat.pdfSupplementary Methods ChIP-chip and data analysis Chromatin

Hybrid On-chip Data Networks

Hybrid On-chip Data Networks

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

Exploring and Understanding ChIP-Seq data · Exploring and Understanding ChIP-Seq data Simon Andrews [email protected] @simon_andrews v2020-05. Data Creation and Processing