1. ChIP-chip Data

2. 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

3. 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

4. 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

5. Transcription Factors General – help to set up transcription of many genes Specific – draw in general factors or RNA Pol II to specific genes TATA Binding Protein

6. DNA Methylation Adding a Methyl to Cytosine Cytosine methylation is passed on to daughter cells

7. Chromatin Immuno-precipitation

8. 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

9. What the data look like histone acetylation on 15 samples over one promoter (raw)

10. Multiple Promoters

11. Normalized by Medians

12. 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?

13. 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

14. MAT One color Affy array –Needs separate array for comparison Normalizes probe thermodynamics & enrichment ratio Estimation by (robust) moving average

15. Normalized Data – Rare Event

16. Normalized Data – Common Event

17. 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 Pol II binding on a 100 bp grid

18. TileMap Ignores normalization ‘Shrinkage’ estimator of variance –Improves individual scores Smooths noise by moving average