Use Case 9: Coordinated Changes of Epigenomic Marks Across Tissue Types. Epigenome Informatics Workshop Bioinformatics Research Laboratory

Transcription

1 Use Case 9: Coordinated Changes of Epigenomic Marks Across Tissue Types Epigenome Informatics Workshop Bioinformatics Research Laboratory 1

2 Introduction Active or inactive states of transcription factor binding elements (promoters, enhancers) may be inferred with certain probability based on the state of a handful of correlated epigenomic marks. H3K9Ac For illustration purposes, this use case will focus on these two marks 2

3 Promoter DNA Methylation in the Human Genome Source of ROIs found in Class: Regulation in the Data Selector Enriched methylated DNA from human primary fibroblasts using methylated DNA immunoprecipitation (MeDIP) + microarray detection 15,609 promoters evaluated in primary somatic and germline cells HCPs (high-cpg promoters) contain 500 bp region with CpG ratio above 0.75 and GC content >55% LCP (low-cpg promoters) do not contain a 500 bp region with a CpG ratio above 0.48 ICP (intermediate CpG promoters) are neither HCPs or LCPs. ICP class contains many subthreshold CpG islands, meaning small CpG islands (<500 bp), moderate CpG richness and/or GC content <55% Weber et al, Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome Nature Genetics, 39 (4), April

4 Examine Transcriptional Regulation Using Promotor ROIs Observation: High (HCP) - and Intermediate CpG (ICP) promoters are regulated by different classes of transcription factors (including Polycomb complex) than Low-CpG (LCP) promoters. HCP, ICP, and LCP promoters may exhibit changes across different epigenomic marks across cell types, or during differentiation (for example, a stem cell line vs a fibroblast cell line). Assessment: Examine differences in H3K9ac and H3K4me3 marks over HCP, ICP, and LCP promoters between an ES cell line (H1) and a fibroblast cell line (IMR90) using data from the Epigenome Atlas. 4

5 Step 1. Go to the Genboree homepage ( and click on Epigenome Atlas

6 Access the Human Epigenome Atlas Data Step 2. Click on Interactive Visualization & Download to launch the grid viewer. 6

7 Select the Tracks of Interest Step 3. Select the tracks/marks of interest (Bisulfite-Seq, Histone H3K4me3, and Histone H3K9ac) for the H1 cell line. Then scroll down and select the same for the IMR90 cell line. 7

8 Save the Selected Tracks to Your Group and Database Step 4. Select your user group (e.g. perwu_group) Step 5. Select the database that you created earlier Step 6. Name this list of tracks Step 7. Click Save Selections to finish selection for current list. 8

9 You will receive notification that your selections are saved. Click on Workbench Data Selector to proceed. 9

10 Step 8. Drag the list of tracks you just created into Input Data Drag 10

11 Drag Step 9. Drag the Promoters:HCP track from the ROI Repository into Input Data Given this set of inputs, Genboree will compare H1 and IMR90 signal intensity (of H3Kme3 and H3KAc9 epigenomic marks, for example) across the high CpG content promoters (the slice ) 11

12 Drag Step 10. Drag your database into the Output Data. This tells Genboree where to deposit the results that will be generated. Note that the Epigenome menu turns green, meaning that it contains a tool(s) that is now active and can operate on what resides in Input Data Step 11. Click on Epigenome, click on Slice Epigenomic Data, click on Download Epigenomic Data Slice 12

13 Step 12. A default Analysis Name is generated by Genboree. It is recommended that all text and the time stamp be kept, and that you append some unique text to the beginning to help you distinguish different jobs run from the same tool. Select (single click) the ROI track displayed Step 13. Click Submit 13

14 You will see the message below upon successful submission of the Data Slice job 14

15 You will receive an with the following message when your job is finished: Clicking on the links will take you to your results. 15

16 Download Results from the Data Selector Step14: Find the result matrix in Files in the Epigenome Slice folder within your target database Step15: Click on the link Click to Download File. Extract the zip file and open it using Excel. 16

17 Epigenomic Slice Tool Data Matrix (unformatted) 17

18 How to Group Epigenomic Slice Tool Output We will re-order the output matrix into the following groups: Bisulfite (2 tracks) H1.BS.Combined IMR90.BS.Combined H1.H3K9ac (5 tracks) H1.H3K9ac.68 H1.H3K9ac.A H1.H3K9ac.62 H1.H3K9ac.40 H1.H3K9ac.26 IMR90.H3K9ac (2 tracks) IMR90.H3K9ac.46 IMR90.H3K9ac.33 H1.H3K4me3 (8 tracks) H1.H3K4me3.12 H1.H3K4me3.A H1.H3K4me3.98 H1.H3K4me3.C H1.H3K4me3.38 H1.H3K4me3.67 H1.H3K4me3.27 H1.H3K4me3.22 IMR90.H3Kme3 (2 tracks) IMR90.H3K4me3.21 IMR90.H3K4me

19 Group Together Columns Corresponding to Replicate Experiments Bisulfite data H1.H3K9ac IMR90.H3K9a c H1.H3K4me3 IMR90.H3K4m e3 Step 16:Group the 19 tracks based on replicate experiment (see slide 18 for breakdown). 19

20 Calculate Average Scores for H1.H3K9ac and for IMR90.H3K9ac from Replicate Experiments H1.H3K9ac (5 tracks) IMR90.H3K9ac (2 tracks) Step 17: Produce averages for each group. 20

21 Calculate the Difference Between the Averages of H1.H3K9ac and IMR90.H3K9ac ( NOTE: use the same method to calculate the difference between the averages of the H3K4me3 signals ) H1.H3K9ac IMR90.H3K9ac Step 18: Calculate difference between H3K9ac and H3K averaged groups. 21

22 Scatter Plot of H3K9ac and H3K4me3 Differences Between H1 and IMR90 over HCP Promoters Difference_H3K9ac Step 19: Produce scatter plot for the two columns representing differences. H3K9ac vs. H3K4me3 (HCP) Difference_H3K4me3 y = x R² = Step 20: Add trend line to scatter plot. Excel 2010 directions: a) Single click the plot b) Click Layout -> Trendline -> Linear Treadline Step 21: Add R^2 value and formula. Excel 2010 directions: a) RIGHT click the trendline b) Click Format Trendline c) Check Display Equation on chart d) Check Display R-squared value on chart 22

23 Use Case 9 Prepared Spreadsheets We have provided the formatted Xls spreadsheets for the following: Use case 9: UseCase9-EpigenomeWorkshopMay2012-matrix_work- HCP-promoters.xls Use case 9 supplement A: UseCase9-EpigenomeWorkshopMay2012-matrix_work- HCP-promoters-1k-subset.xls 23

24 Use Case 9 Supplementary Work Try the same use case 9 work flow, but with the following ROI tracks: A. Promoters:HCP (1k subset) B. Promoters:ICP C. Promoters:LCP Can you reproduce the following plots? 24

25 Scatter Plot of H3K9ac and H3K4me3 Differences Between H1 and IMR90 over HCP (1k subset) 25

26 Scatter Plot of H3K9ac and H3K4me3 Differences Between H1 and IMR90 over ICP and LCP Promoters H3K9ac vs H3K4me3 (ICP) y = 2.306x R² = Difference_H3K9ac (H1-IMR90) Difference_H3K4me3 (H1-IMR90) Difference_H3K9ac (H1-IMR90) H3K9ac vs H3K4me3 (LCP) y = x R² = Difference_H3K4me3 (H1-IMR90) 26