# PEREpigenomics Profile Explorer of Roadmap Epigenomics data

Guillaume Devailly

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## To cite this version:

Guillaume Devailly. PEREpigenomics Profile Explorer of Roadmap Epigenomics data. UseR! 2019, Jul 2019, Toulouse, France. **hal-02289519**

HAL Id: hal-02289519

https://hal.science/hal-02289519

Submitted on 5 Jun 2020

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Distributed under a Creative Commons Attribution 4.0 International License
# PEREpigenomics

## Profile Explorer of Roadmap Epigenomics data

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Guillaume Devailly

useR!2019

2019/07/09

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GenPhySE

Génétique, Physiologie et Systèmes d'Elevage

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INRA
SCIENCE & IMPACT
One genome, many cell types

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Differential gene expression =
cellular environment + epigenetics
Many existing datasets and databases.

**Dataset:**

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* RNA-seq

* DNAse1

* WGBS,

* 10 different histone methylations

* 17 different histone acetylations

in 33 human cell lines & tissues,
uniformly processed.

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Link data to genome browser:

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Copyright © 2018-2019 Washington University in St. Louis. All rights reserved.

Developed by the **Wang Lab**

Terms and Conditions of Use
# What to do with big dataset?

## Machine learning:

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Kundaje, Meuleman, Ernst, Bilenky et al., 2015, 10.1038/nature14248
* Visualisation of marks, sorted by **gene** transcription level:

* at TSS (gene start)

* at TTS (gene end)

* Visualisation of marks at **middle exons** starts, sorted by:

* transcription level

* inclusion ratio

* For **all** genes/exons in **each** cell type.

* For **each** gene/exon in **all** cell types.

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H3K4me3, TSS, small intestine
# Different gene types, different associations

## lincRNA

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## processed pseudogenes

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Exonic mark: H3K36me3, fetal large intestine

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DNA methylation: ratio and density

CpG
density

mCpG %

mCpG
density

WGBS
coverage

CGI

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# Exonic DNA methylation

## WGBS, pancreas

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Cell by cell vs gene by gene

WGBS, adult liver

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mCpG ratio

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H3K4me3

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Too many plots?

<figure><img src="image_33.png" /><figcaption>Figure 1: Epigenetic marks at promoters and transcription level in H1 embryonic stem cells</figcaption></figure>

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Profile Explorer of Roadmap Epigenomic data

www.perepigenomics.roslin.ed.ac.uk

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Summary of results

<table><thead><tr><th>mark</th><th>cell type by cell type</th><th>gene by gene</th><th>center on TSS</th></tr></thead><tbody><tr><td>WGBS</td><td>negative</td><td>negative</td><td></td></tr><tr><td>DNAse</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H2A.Z</td><td>positive</td><td>balanced</td><td></td></tr><tr><td>H3K4me1</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K4me2</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K4me3</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K9me3</td><td>unclear</td><td>unclear</td><td>no</td></tr><tr><td>H3K23me2</td><td>positive</td><td>NA</td><td></td></tr><tr><td>H3K27me3</td><td>negative - variable</td><td>negative</td><td></td></tr><tr><td>H3K36me3</td><td>positive</td><td>positive</td><td>no</td></tr><tr><td>H3K79me1</td><td>positive</td><td>positive</td><td>no</td></tr><tr><td>H3K79me2</td><td>positive</td><td>balanced</td><td>no</td></tr></tbody></table>

<table><thead><tr><th>mark</th><th>cell type by cell type</th><th>gene by gene</th><th>center on TSS</th></tr></thead><tbody><tr><td>H2AK5ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H2BK120ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H2BK12ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H2BK15ac</td><td>positive</td><td>balanced</td><td></td></tr><tr><td>H2BK20ac</td><td>neutral</td><td>NA</td><td></td></tr><tr><td>H2BK5ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K4ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K9ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K14ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K18ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K23ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K27ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H3K56ac</td><td>positive</td><td>NA</td><td></td></tr><tr><td>H4K8ac</td><td>positive</td><td>positive</td><td></td></tr><tr><td>H4K12ac</td><td>positive</td><td>NA</td><td></td></tr><tr><td>H4K91ac</td><td>positive</td><td>positive</td><td></td></tr></tbody></table>
Conclusions

PEREpigenomics offers interesting visualisations of epigenetic data gathered by
Roadmap Epigenomics.

Perspectives

* update with new annotation data (ongoing)

* preprint & source code available soon

* develop similar approach for **FAANG** (Functional Annotation of the Animal Genomes) data
Anagha Joshi

Anna Mantsoki

Deepti Vipin

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GenPhySE

Génétique, Physiologie et Systèmes d'Élevage

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INRA
SCIENCE & IMPACT

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ROADMAP
epigenomics
PROJECT

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PROSLIN

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THE UNIVERSITY
of EDINBURGH

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BBSRC

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CASCADE-FELLOWS

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CREATED WITH

bio
RENDER

WWW.BIORENDER.COM