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Transcript 
Bioinformatic Tools for
Epigenetic Research
Mehmet Tevfik DORAK, MD PhD
2nd Practical Bioinformatics Course
Istanbul, 17/18 April 2017
YOUR FUTURE
STARTS WITH HOPE
Schedule
Epigenetics
Transcriptional regulation:
- DNA methylation
Post-transcriptional regulation:
- Non-coding RNA or RNA-binding protein interference
- Histone modifications
- Nuclear (chromatin) arrangements (3D genome)
Epigenetics
Protein expression is regulated more by post-transcriptional modifications
reducing the correlation between transcription levels and protein levels.
Epigenetics
Epigenetics: Bioinformatic Tools
Epigenetics: Bioinformatic Tools
Epigenetics: rVarBase
Epigenetics: rVarBase
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 ***
Epigenetics: Drug Effects
Epigenetics: Chromatin States
Epigenetics: Chromatin States
… Looking forward …..
YOUR FUTURE
STARTS WITH HOPE
YOUR FUTURE
STARTS WITH HOPE
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