IDEAS Roadmap Track Settings
 
IDEAS segmentation using Roadmap

Display mode:       Reset to defaults   

Show only items with score at or above:   (range: 0 to 1000)


Display data as a density graph:

Select subtracks by type: (help)
Type
IMR90
ESC
iPSC
ES-deriv
Blood and T-cell
HSC and B-cell
Mesench
Myosat
Epithelial
Neurosph
Thymus
Brain
Adipose
Muscle
Heart
Sm. Muscle
Digestive
Other
ENCODE2012
List subtracks: only selected/visible    all    ()  
dense
 Configure 		 E002_ESC.WA7  E002_ES-WA7 Cells   Data format 
dense
 Configure 		 E008_ESC.H9  E008_H9 Cells   Data format 
dense
 Configure 		 E001_ESC.I3  E001_ES-I3 Cells   Data format 
dense
 Configure 		 E003_ESC.H1  E003_H1 Cells   Data format 
dense
 Configure 		 E007_ESDR.H1.NEUR.PROG  E007_H1 Derived Neuronal Progenitor Cultured Cells   Data format 
dense
 Configure 		 E009_ESDR.H9.NEUR.PROG  E009_H9 Derived Neuronal Progenitor Cultured Cells   Data format 
dense
 Configure 		 E010_ESDR.H9.NEUR  E010_H9 Derived Neuron Cultured Cells   Data format 
dense
 Configure 		 E013_ESDR.CD56.MESO  E013_hESC Derived CD56+ Mesoderm Cultured Cells   Data format 
dense
 Configure 		 E012_ESDR.CD56.ECTO  E012_hESC Derived CD56+ Ectoderm Cultured Cells   Data format 
dense
 Configure 		 E011_ESDR.CD184.ENDO  E011_hESC Derived CD184+ Endoderm Cultured Cells   Data format 
dense
 Configure 		 E004_ESDR.H1.BMP4.MESO  E004_H1 BMP4 Derived Mesendoderm Cultured Cells   Data format 
dense
 Configure 		 E005_ESDR.H1.BMP4.TROP  E005_H1 BMP4 Derived Trophoblast Cultured Cells   Data format 
dense
 Configure 		 E006_ESDR.H1.MSC  E006_H1 Derived Mesenchymal Stem Cells   Data format 
    
Assembly: Human Feb. 2009 (GRCh37/hg19)

Description

The Integrative and Discriminative EPigenome Annotation System (IDEAS) method for simultaneous two-dimensional segmentation (Zhang et al. NAR 2016; Zhang and Hardison, NAR 2017) was used to run on 5 epigenetic marks (H3K4me3, H3K4me1, H3K36me3, H3K27me3, H3K9me3) in 127 cell types in the Roadmap Epigenomics project. For this segmentation by IDEAS, the -log10 pval tracks were used as input. We used a pipeline to improve the reproducibility of the functional annotation (Zhang and Hardison, NAR 2017). For this run on 5 features in 127 cell types, the reproducibility cut off was set at 90%.

Display Conventions and Configuration

The contributions of each epigenetic feature to each of the 20 states is shown in the figure, along with the color code and their abundance in 127 cell types. Briefly, warm colors are associated with activity and cold colors with inactivity. In more detail, red denotes a state with a promoter-like signature, yellow denote states with an enhancer-like signature, and green denotes a signature for elongating RNA polymerase. In contrast, the grey states convey various combinations of no to low signals for any of the features, and blue states generally correspond to repressive signals.

State Color Key:

state color

Data source

http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/

Contact

Questions should be sent to Yu Zhang at yzz2 at psu dot edu

References

Zhang Y, Ross C Hardison. (2017) Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. Nucleic Acids Res. gkx659. DOI: https://doi.org/10.1093/nar/gkx659

Zhang Y, An L, Yue F, Hardison RC (2016). Jointly characterizing epigenetic dynamics across multiple human cell types. Nucleic Acids Res. 44(14):6721-31.