zlab-annotations.umassmed.edu

ENCODE Annotations V3

60; Encyclopedia (v3). Candidate enhancers based on DNase and H3K27ac signals. Search Enhancer-like Regions (v3). Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Enter gene, SNP,. Coordinate, or rank. Gene, SNP (ex. rs11742570. Genomic region, or peak rank. Gene, SNP (ex. rs27106747. Genomic region, or peak rank. Candidate enhancers computed using DNase and H3K27ac signals for cell types below (genome wide). IPS DF 6.9 Cells. Primary hem...

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ENCODE Annotations V3 | zlab-annotations.umassmed.edu Reviews

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60; Encyclopedia (v3). Candidate enhancers based on DNase and H3K27ac signals. Search Enhancer-like Regions (v3). Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Enter gene, SNP,. Coordinate, or rank. Gene, SNP (ex. rs11742570. Genomic region, or peak rank. Gene, SNP (ex. rs27106747. Genomic region, or peak rank. Candidate enhancers computed using DNase and H3K27ac signals for cell types below (genome wide). IPS DF 6.9 Cells. Primary hem...

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1 enhancer like

2 promoter like

3 interacting genes

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8 examples

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ENCODE Annotations V3 | zlab-annotations.umassmed.edu Reviews

https://zlab-annotations.umassmed.edu

60; Encyclopedia (v3). Candidate enhancers based on DNase and H3K27ac signals. Search Enhancer-like Regions (v3). Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Enter gene, SNP,. Coordinate, or rank. Gene, SNP (ex. rs11742570. Genomic region, or peak rank. Gene, SNP (ex. rs27106747. Genomic region, or peak rank. Candidate enhancers computed using DNase and H3K27ac signals for cell types below (genome wide). IPS DF 6.9 Cells. Primary hem...

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zlab-annotations.umassmed.edu

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ENCODE Annotations V3

http://zlab-annotations.umassmed.edu/interacting_gene

60; Encyclopedia (v3). Search Interacting Gene Regions. Visualize on Genome Browser. Enter gene, SNP,. Coordinate, or rank. Gene, SNP (ex. rs149273678. Genomic region, or peak rank.

2

ENCODE Annotations V3

http://zlab-annotations.umassmed.edu/tutorial

60; Encyclopedia (v3). Enter gene, SNP, genomic coordinate, or rank. Choose assays used to determine enhancer-like elements. Select cell types of interest. Cell types: hindbrain, midbrain, neural tube, and lung. Display on genome browser. You are a graduate student working on the mechanistic role and therapeutic potential of microRNA-122 (MIR122) in alcoholic liver disease. Are there any enhancers nearby that you could potentially study? Visualize on Genome Browser. Visualize on Genome Browser.

3

ENCODE Annotations V3

http://zlab-annotations.umassmed.edu/promoters

60; Encyclopedia (v3). Promoter-like regions based on DNase and H3K4me3 signals. Search Promoter-like Regions (v3). Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Enter gene, SNP,. Coordinate, or rank. Gene, SNP (ex. rs11742570. Genomic region, or peak rank. Gene, SNP (ex. rs27106747. Genomic region, or peak rank. Candidate enhancers computed using DNase and H3K4me3 signals for cell types below (genome wide). B cell (adult 43 year).

4

ENCODE Annotations V3

http://zlab-annotations.umassmed.edu/enhancers/methods

60; Encyclopedia (v3). Enhancer-like regions based on DNase and H3K27ac signals. Across four mouse tissues (midbrain, hindbrain, neural tube, and limb) at the embryonic day 11.5 (E11.5), anchoring predictions on DNase peaks outperforms anchoring predictions on H3K27ac peaks. We also found that ranking predictions by a combination of H3K27ac signal and DNase signal performed the best (Figure 1). Method for predicting enhancer-like regions.

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ENCODE Annotations V3

60; Encyclopedia (v3). Candidate enhancers based on DNase and H3K27ac signals. Search Enhancer-like Regions (v3). Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Visualize on Genome Browser. Enter gene, SNP,. Coordinate, or rank. Gene, SNP (ex. rs11742570. Genomic region, or peak rank. Gene, SNP (ex. rs27106747. Genomic region, or peak rank. Candidate enhancers computed using DNase and H3K27ac signals for cell types below (genome wide). IPS DF 6.9 Cells. Primary hem...

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