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DevelopmentalStages_SegmentTypes

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Select subtracks by segmenttype and stage: (help)
 All SegmentType ChromHMM  PADREs  consensus PADREs  DOPEs 
Stage
Dome 
Epi75 
03 5-9 somites 
Prim5 
LongPec 
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  SegmentType↓1 Stage↓2   Track Name↓3  
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 ChromHMM  03 5-9 somites  CHMM_5-9_somites   Schema 
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 ChromHMM  Dome  CHMM_Dome   Schema 
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 ChromHMM  Epi75  CHMM_Epi75   Schema 
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 ChromHMM  LongPec  CHMM_LongPec   Schema 
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 ChromHMM  Prim5  CHMM_Prim5   Schema 
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 consensus PADREs  03 5-9 somites  cPADRE_5-9_somites   Schema 
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 consensus PADREs  Dome  cPADRE_Dome   Schema 
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 consensus PADREs  Epi75  cPADRE_Epi75   Schema 
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 consensus PADREs  LongPec  cPADRE_LongPec   Schema 
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 consensus PADREs  Prim5  cPADRE_Prim5   Schema 
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 DOPEs  03 5-9 somites  DOPEs_5-9_somites   Schema 
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 DOPEs  Dome  DOPEs_Dome   Schema 
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 DOPEs  Epi75  DOPEs_Epi75   Schema 
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 DOPEs  LongPec  DOPEs_LongPec   Schema 
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 DOPEs  Prim5  DOPEs_Prim5   Schema 
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 PADREs  03 5-9 somites  PADREs_5-9_somites   Schema 
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 PADREs  Dome  PADREs_Dome   Schema 
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 PADREs  Epi75  PADREs_Epi75   Schema 
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 PADREs  LongPec  PADREs_LongPec   Schema 
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 PADREs  Prim5  PADREs_Prim5   Schema 
    

Regulatory elements tracks

This collection of tracks contains annotation tracks for regulatory elements defined by different methods.

  • ChromHMM: A classification of genomic regions based on chromatin marks.
    Classes:
    1. TssA1: Active Transcription Start Site
    2. TssA2: Active Transcription Start Site
    3. TssFlank1: Transcription Start Site flanking region
    4. TssFlank2: Transcription Start Site flanking region
    5. EnhA1: Active enhancer
    6. EnhFlank: Flanking Enhancer
    7. EnhWk1: Weak Enhancer
    8. Pois: Poised elements
    9. ReprPC: PolyComb repressed regions
    10. Quies: Quiescent state
  • PADREs: Reproducible open chromatin regions classified based on presence of CRE-associated histone modification marks (H3K4me3, H3K4me1, H3K27ac, and H3K27me3) with ChromHMM.
    • Classes:
    1. TssA1: Active Transcription Start Site
    2. TssA2: Active Transcription Start Site
    3. TssFlank1: Transcription Start Site flanking region
    4. TssFlank2: Transcription Start Site flanking region
    5. EnhA1: Active enhancer
    6. EnhFlank: Flanking Enhancer
    7. EnhWk1: Weak Enhancer
    8. Pois: Poised elements
    9. ReprPC: PolyComb repressed regions
    10. Quies: Quiescent state
  • consensus PADREs: PADREs which are open in at least two stages.
  • DOPEs: Stage-specific open chromatin without histone marks (quiescent PADREs).

For more information about the different methods, see our publication: Baranasic, Damir, et al. "Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish."