1. Bioinformatic Tools for Epigenetic Research
Mehmet Tevfik DORAK, MD PhD
2nd Practical Bioinformatics Course
Istanbul, 17/18 April 2017

2. Schedule

3. Epigenetics Transcriptional regulation:
- DNA methylation
Post-transcriptional regulation:
- Non-coding RNA or RNA-binding protein interference
- Histone modifications
- Nuclear (chromatin) arrangements (3D genome)

4. Epigenetics
Link:
Protein expression is regulated more by post-transcriptional modifications reducing the correlation between transcription levels and protein levels.

5. Epigenetics
Link:

6. Epigenetics: Bioinformatic Tools

7. Epigenetics: Bioinformatic Tools
EpiGenie:

8. Epigenetics: rVarBase
Paper:

9. Epigenetics: rVarBase
Paper:

10. Epigenetics: Post-transcriptional effects
RBP-Var is a database for annotation of functional variants which potentiall influence on RNA-protein interactions by changing RNA structure.
It contains dbSNPs in RBP bindig sites (rbSNPs), secondary structure change by SNP (RiboSNitch), the binding sites of miRNA and potential functional SNPs which can impact RBP binding.
In addition, RBP-Var also integrates GWAS data, eQTL data, ClinVar data, and COSMIC data into selection of functional SNP for genetic association studies.
*** It analyzes LD proxies, and scores variants ***
Link: (try TFRC rs )
Paper:

11. Epigenetics: Drug Effects
HEDD: (try resveratrol)
Paper:

12. Epigenetics: Chromatin States
Links:

13. Epigenetics: Chromatin States
Link:

14. … Looking forward …..