Organized By Mark RNA Track Settings
 
RNA tracks from Craniofacial Data

Track collection: Cotney Craniofacial hub organized by mark

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+  All tracks in this collection (15)

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CS13-12690 
CS13-13365 
CS13-13472 
CS14-12408 
CS14-12704 
CS14-12913 
CS15-13000 
CS15-13019 
CS15-13128 
CS17-12320 
CS17-12421 
CS17-12588 
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H9-1 
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H9-3 
CNCC-1 
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CNCC-3 
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 RNA  CNCC-1  CNCC-1RNA   Data format 
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 RNA  CNCC-2  CNCC-2RNA   Data format 
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 RNA  CNCC-3  CNCC-3RNA   Data format 
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 RNA  CS13-12690  CS13-12690RNA   Data format 
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 RNA  CS13-13365  CS13-13365RNA   Data format 
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 RNA  CS13-13472  CS13-13472RNA   Data format 
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 RNA  CS14-12408  CS14-12408RNA   Data format 
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 RNA  CS14-12704  CS14-12704RNA   Data format 
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 RNA  CS14-12913  CS14-12913RNA   Data format 
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 RNA  CS15-13000  CS15-13000RNA   Data format 
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 RNA  CS15-13019  CS15-13019RNA   Data format 
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 RNA  CS15-13128  CS15-13128RNA   Data format 
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 RNA  CS17-12320  CS17-12320RNA   Data format 
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 RNA  CS17-12421  CS17-12421RNA   Data format 
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 RNA  CS17-12588  CS17-12588RNA   Data format 
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 RNA  CS22 PE FB  CS22_PE_FBRNA   Data format 
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 RNA  CS22 SE FB  CS22_SE_FBRNA   Data format 
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 RNA  H9-1  H9-1RNA   Data format 
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 RNA  H9-2  H9-2RNA   Data format 
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 RNA  H9-3  H9-3RNA   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

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.