loading

Data Analysis

Build BED files for genomic regions enrichment analysis
Form Elements
: - Example: chr1:4763278-4775807
expanding (upstream of the TSS): 20 kb 50 kb 100 kb other bp Example: MFN2 ( NM_001127660 )
Example: hg19_H1_chr6_32935594
Special examples

1 All super-enhancers on "chr1" in SEA:

Human (hg19)

2 Gene symbol

Human (SOX2)

3 Genome location

Human (chr1:11890229-12223579)

4 Super-enhancer name/ID

Mouse (mm9_Heart_3_chr9_3002875)





Specific analysis of H3K27ac status in super-enhancer regions
Form Elements
It was required that at least one cell type/tissue should be selected as the analysis object. Considering the computing performance and waiting time, we suggest that choosing no more than 20 cell types if the number of the submitted regions is larger than 100, or submitting no more than 10 regions if users select all the cell types listed in the Data Analysis page.
Example: chr1:4763278-4775807 (one per row)
No file selected Choose File
Please, upload a BED file. Example BED
Note:

It is time-consuming for analysis large datasets.

It needs about 3 seconds per genome region and per tissue/cell type. What should be mentioned is that there maybe more than one dataset for each tissue/cell type.

For test, we submited the "Example BED" files with 8 human (hg19) genome regions, and selected all the 99 tissue/cell types. Then, it takes more than 40 minutes to get the result of overlap table and heeatmap for average status of H3K27ac.

Example for Regions:

chr3:181403691-181476186

chr3:181403893-181455295

chr3:181404243-181455400

File Format:

#bed file description

#<chrom> <start> <end> <region discription>

chr3 181403691 181476186 region_1

chr3 181403893 181455295 region_2

chr3 181404243 181455400 region_3

Enrichment analysis of Transcription factors in the super enhancers
Form Elements
: - Example: chr1:4763278-4775807
expanding (upstream of the TSS): 20 kb 50 kb 100 kb other bp Example: MFN2 ( NM_001127660 )
Example: hg19_H1_chr6_32935594
Whole genome
BED file:
No file selected Choose File
When should I use a background set? What should my background regions file contain?