Organized By Mark Tracks
 
Cotney Craniofacial hub organized by mark tracks

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 All
25_State_Gateway_Superenhancers  25_State_Dense_Gateway_Superenhancers  
ChromHMM  Chromatin State tracks from Craniofacial Data  
DNase  DNase tracks from Craniofacial Data  
H2AZ  H2AZ tracks from Craniofacial Data  
H3K27ac  H3K27ac tracks from Craniofacial Data  
H3K27me3  H3K27me3 tracks from Craniofacial Data  
H3K36me3  H3K36me3 tracks from Craniofacial Data  
H3K4me1  H3K4me1 tracks from Craniofacial Data  
H3K4me2  H3K4me2 tracks from Craniofacial Data  
H3K4me3  H3K4me3 tracks from Craniofacial Data  
H3K79me2  H3K79me2 tracks from Craniofacial Data  
H3K9ac  H3K9ac tracks from Craniofacial Data  
H3K9me3  H3K9me3 tracks from Craniofacial Data  
H4K20me1  H4K20me1 tracks from Craniofacial Data  
Assembly: Human Feb. 2009 (GRCh37/hg19)

Emma Wentworth at UCONN HEALTH built this track, and the Cotney Lab is responsible for its contents.

Gene Expression

Gene expression data can be fully explored on a shinyapp at Craniofacial Gene Expression Explorer

Display conventions

Each track can be turned on/off individually. All tracks displays read density data in form of wiggle plots. For Histone/DNase, there also enrichment signal tracks using MACS based on pvalue or fold Change. There are also imputed signal for segmentations tracks.

Histone/DNase Signal/Peak Color Legend

  • DNase -  DNase 
  • H2A.Z -  H2A.Z 
  • H3K27ac -  H3K27ac 
  • H3K27me3 -  H3K27me3 
  • H3K36me3 -  H3K36me3 
  • H3K4me1 -  H3K4me1 
  • H3K4me2 -  H3K4me2 
  • H3K4me3 -  H3K4me3 
  • H3K79me2 -  H3K79me2 
  • H3K9ac -  H3K9ac 
  • H3K9me3 -  H3K9me3 
  • H4K20me1 -  H4K20me1 

Primary Core Marks segmentation

  • State 1 -  Red  - TssA (Active_TSS)
  • State 2 -  OrangeRed  - TssAFlnk (Flanking_Active_TSS)
  • State 3 -  LimeGreen  - TxFlnk (Transcr_at_gene_5_and_3primer)
  • State 4 -  Green  - Tx (Strong_transcription)
  • State 5 -  DarkGreen  - TxWk (Weak_transcription)
  • State 6 -  GreenYellow  - EnhG (Genic_enhancers)
  • State 7 -  Yellow  - Enh (Enhancers)
  • State 8 -  MediumAquamarine  - ZNF/Rpts (ZNF_genes&repeats)
  • State 9 -  PaleTurquoise  - Het (Heterochromatin)
  • State 10 -  IndianRed  - TssBiv (Bivalent/Poised_TSS)
  • State 11 -  DarkSalmon  - BivFlnk (Flanking_Bivalent_TSS/Enh)
  • State 12 -  DarkKhaki  - EnhBiv (Bivalent_Enhancer)
  • State 13 -  Silver  - ReprPC (Repressed_PolyComb)
  • State 14 -  Gainsboro  - ReprPCWk (Weak_Repressed_PolyComb)
  • State 15 -  White  - Quies (Quiescent/Low)

Auxiliary Core Marks + K27ac segmentation

  • State 1 -  Red  - TssA (Active_TSS)
  • State 2 -  Orange_Red  - TssFlnk (Flanking_TSS)
  • State 3 -  Orange_Red  - TssFlnkU (Flanking_TSS_Upstream)
  • State 4 -  Orange_Red  - TssFlnkD (Flanking_TSS_Downstream)
  • State 5 -  Green  - Tx (Strong_transcription)
  • State 6 -  DarkGreen  - TxWk (Weak_transcription)
  • State 7 -  GreenYellow  - EnhG1 (Genic_enhancer1)
  • State 8 -  GreenYellow  - EnhG2 (Genic_enhancer2)
  • State 9 -  Orange  - EnhA1 (Active_Enhancer1)
  • State 10 -  Orange  - EnhA2 (Active_Enhancer2)
  • State 11 -  Yellow  - EnhWk (Weak_Enhancer)
  • State 12 -  Medium_Aquamarine  - ZNF/Rpts (ZNF_genes&repeats)
  • State 13 -  PaleTurquoise  - Het (Heterochromatin)
  • State 14 -  IndianRed  - TssBiv (Bivalent/Poised_TSS)
  • State 15 -  DarkKhaki  - EnhBiv (Bivalent_Enhancer)
  • State 16 -  Silver  - ReprPC (Repressed_PolyComb)
  • State 17 -  Gainsboro  - ReprPCWk (Weak_Repressed_PolyComb)
  • State 18 -  White  - Quies (Quiescent/Low)

Imputed Marks Segmentation

  • State 1 -  Red  - TssA (Active TSS)
  • State 2 -  Orange Red  - PromU (Promoter Upstream TSS)
  • State 3 -  Orange Red  - PromD1 (Promoter Downstream TSS with DNase)
  • State 4 -  Orange Red  - PromD2 (Promoter Downstream TSS)
  • State 5 -  Green  - Tx5' (Transcription 5')
  • State 6 -  Green  - Tx (Transcription)
  • State 7 -  Green  - Tx3' (Transcription 3')
  • State 8 -  Light Green  - TxWk (Weak transcription)
  • State 9 -  GreenYellow  - TxReg (Transcription Regulatory)
  • State 10 -  GreenYellow  - TxEnh5' (Transcription 5' Enhancer)
  • State 11 -  GreenYellow  - TxEnh3' (Transcription 3' Enhancer)
  • State 12 -  GreenYellow  - TxEnhW (Transcription Weak Enhancer)
  • State 13 -  Orange  - EnhA1 (Active Enhancer 1)
  • State 14 -  Orange  - EnhA2 (Active Enhancer 2)
  • State 15 -  Orange  - EnhAF (Active Enhancer Flank)
  • State 16 -  Yellow  - EnhW1 (Weak Enhancer 1)
  • State 17 -  Yellow  - EnhW2 (Weak Enhancer 2)
  • State 18 -  Yellow  - EnhAc (Enhancer Acetylation Only)
  • State 19 -  Light Yellow  - DNase (DNase only)
  • State 20 -  Medium Aquamarine  - ZNF/Rpts (ZNF genes & repeats)
  • State 21 -  PaleTurquoise  - Het (Heterochromatin)
  • State 22 -  Light Purple  - PromP (Poised Promoter)
  • State 23 -  Purple  - PromBiv (Bivalent Promoter)
  • State 24 -  Silver  - ReprPC (Repressed PolyComb)
  • State 25 -  White  - Quies (Quiescent/Low)

Contacts

Please email Justin Cotney for questions.