ENCODE element browser and 3D genome browser
Feng Yue, PhD Assistant Professor
Dept. of Biochemistry & Molecular Biology School of Medicine
Penn State University
Outline
1. Search and visualize ENCODE annotations (gene
expression, candidate promoters, enhancers …)
2. Visualize ENCODE chromatin interaction data
(Hi-C, ChIA-PET)
ENCODE element query website
ENCODE element query website
Click human tab, and search for the expression for Sox2
Visualize and save the gene expression profile
You can choose the cell types to display!
You can choose the cell types to display!
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
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)
Transcriptional regulation by cis-regulatory elements
Promoter
Co-activator
Enhancer
TF TF
RNA pol Gene transcription
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
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
Hi-C measures genome-wide chromatin interaction
http://3dgenome.org
Users can query by gene name or genomic loci
Navigation bars to explore Hi-C data
Built-in genome browser session
You can use your own Hi-C data - no need to upload!
Visualize your own Hi-C data
Use virtual 4C to hypothesize the enhancer promoter interaction
Virtual 4C is derived from Hi-C matrix
Jin et al, Nature, 2013
Summary
1. Search and visualize ENCODE annotations (gene
expression, promoters, enhancers …)
2. Visualize ENCODE chromatin interaction data
(Hi-C, ChIA-PET)
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 …