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chromHMM

epigenome states

 

Core 15-state model

 

 

STATE NO. MNEMONIC DESCRIPTION COLOR NAME COLOR CODE
1 TssA Active TSS Red 255,0,0
2 TssAFlnk Flanking Active TSS Orange Red 255,69,0
3 TxFlnk Transcr. at gene 5' and 3' LimeGreen 50,205,50
4 Tx Strong transcription Green 0,128,0
5 TxWk Weak transcription DarkGreen 0,100,0
6 EnhG Genic enhancers GreenYellow 194,225,5
7 Enh Enhancers Yellow 255,255,0
8 ZNF/Rpts ZNF genes & repeats Medium Aquamarine 102,205,170
9 Het Heterochromatin PaleTurquoise 138,145,208
10 TssBiv Bivalent/Poised TSS IndianRed 205,92,92
11 BivFlnk Flanking Bivalent TSS/Enh DarkSalmon 233,150,122
12 EnhBiv Bivalent Enhancer DarkKhaki 189,183,107
13 ReprPC Repressed PolyComb Silver 128,128,128
14 ReprPCWk Weak Repressed PolyComb Gainsboro 192,192,192
15 Quies Quiescent/Low White 255,255,255

 

 

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Expanded 18-state model

 

The states are as follows

STATE NO. MNEMONIC DESCRIPTION COLOR NAME COLOR CODE
1 TssA Active TSS Red 255,0,0
2 TssFlnk Flanking TSS Orange Red 255,69,0
3 TssFlnkU Flanking TSS Upstream Orange Red 255,69,0
4 TssFlnkD Flanking TSS Downstream Orange Red 255,69,0
5 Tx Strong transcription Green 0,128,0
6 TxWk Weak transcription DarkGreen 0,100,0
7 EnhG1 Genic enhancer1 GreenYellow 194,225,5
8 EnhG2 Genic enhancer2 GreenYellow 194,225,5
9 EnhA1 Active Enhancer 1 Orange 255,195,77
10 EnhA2 Active Enhancer 2 Orange 255,195,77
11 EnhWk Weak Enhancer Yellow 255,255,0
12 ZNF/Rpts ZNF genes & repeats Medium Aquamarine 102,205,170
13 Het Heterochromatin PaleTurquoise 138,145,208
14 TssBiv Bivalent/Poised TSS IndianRed 205,92,92
15 EnhBiv Bivalent Enhancer DarkKhaki 189,183,107
16 ReprPC Repressed PolyComb Silver 128,128,128
17 ReprPCWk Weak Repressed PolyComb Gainsboro 192,192,192
18 Quies Quiescent/Low White 255,255,255

 

 

 

  • epigenome states