ENCODE element browser and 3D genome browser

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ENCODE element browser and 3D genome browser Feng Yue, PhD Assistant Professor Dept. of Biochemistry & Molecular Biology School of Medicine Penn State University

Transcript of ENCODE element browser and 3D genome browser

Page 1: ENCODE element browser and 3D genome browser

ENCODE element browser and 3D genome browser

Feng Yue, PhD Assistant Professor

Dept. of Biochemistry & Molecular Biology School of Medicine

Penn State University

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Outline

1.  Search and visualize ENCODE annotations (gene

expression, candidate promoters, enhancers …)

2.  Visualize ENCODE chromatin interaction data

(Hi-C, ChIA-PET)

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ENCODE element query website

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ENCODE element query website

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Click human tab, and search for the expression for Sox2

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Visualize and save the gene expression profile

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You can choose the cell types to display!

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You can choose the cell types to display!

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Linking enhancers to target promoters Enhancer

Bone Marrow Cerebellum Cortex Heart Kidney Liver Lung Mef ES Spleen

Correlation coefficient

Correlation coefficient

DNaseI DNase I DNaseI

Gene 1 Gene 2

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Outline for the workshop

1.  Search and download through ENCODE portal

2.  Search and visualize ENCODE annotations (gene

expression, promoters, enhancers …)

3.  Visualize ENCODE chromatin interaction data

(Hi-C, ChIA-PET)

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Transcriptional regulation by cis-regulatory elements

Promoter

Co-activator

Enhancer

TF TF

RNA pol Gene transcription

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Chromatin conformation capture (3C) experiment

Enhancer

Gene transcription

Promoter

TF TF

Anchor Primer2 primer3 Primer 1

3C experiment

Anchor Primer2 primer3 Primer 1

3C experiment

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Hi-C measures genome-wide chromatin interaction

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_-

_-

_-

_3

0.2

0.25

0.55

0.35

Foxg1

400 kb51000000Chr12

0

40

Normalizedinteraction freq.

Dixon et al. nature, 2012

H3K4me3

RNA polII

CTCF

H3K4me1

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Hi-C measures genome-wide chromatin interaction

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http://3dgenome.org

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Users can query by gene name or genomic loci

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Navigation bars to explore Hi-C data

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Built-in genome browser session

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You can use your own Hi-C data - no need to upload!

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Visualize your own Hi-C data

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Use virtual 4C to hypothesize the enhancer promoter interaction

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Virtual 4C is derived from Hi-C matrix

Jin et al, Nature, 2013

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Summary

1.  Search and visualize ENCODE annotations (gene

expression, promoters, enhancers …)

2.  Visualize ENCODE chromatin interaction data

(Hi-C, ChIA-PET)

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Acknowledgement

ENCODE consortium ENCODE DCC

- Mike Cherry - Seth Strattan - Ben Hitz - Aditi Kalpagam Narayanan …

ENCODE EDAC - Zhiping Weng …

Yue Lab - Yanli Wang - Lijun Zhang - GalYaroslavsky - Tyler Derr

Dr. Bing Ren

and many others …