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.
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