encode element browser and 3d genome browser
TRANSCRIPT
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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
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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
-
_-
_-
_-
_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)
![Page 35: ENCODE element browser and 3D genome browser](https://reader030.vdocuments.mx/reader030/viewer/2022012720/61b313a4a8caa77f6f5c22b6/html5/thumbnails/35.jpg)
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 …