Human Epigenome Browser

↓ Genomic view

Scaffold sequence

Gene Set View

Juxtaposition

↓ Tracks

Genome heatmap

Genomic annotation

Custom track

↓ Statistics & analysis

Correlation

Pairwise comparison

Hypothesis test

Session

Config & Misc

Cite us

Genomic annotation tracks

New! Try the long-range interaction tracks

☃

Use drop-down menu to toggle track display mode,
click ✕ to remove from list,
click "Add more" button to add to list.

Custom tracks

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GO BACK

bedGraph

quantitative data

bigWig

quantitative data

BED

annotation data

BED ⋒

long-range interaction data

SAM

read alignment data

DataHub

batch submission

Manage (0)

everything goes here

bedGraph file must be compressed by bgzip and indexed by tabix. Learn more ↗

bedGraph file URL

The index file must be accessible from the same path
If bedgraph file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

Selected terms will be listed below

this step is optional

bigWig↗ file URL

Track name

Selected terms will be listed below

this step is optional

bigBed files are no longer supported, use BED files instead (tabix indexed). Learn more ↗

BED file URL

The index file must be accessible from the same path
If bed file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

Display mode

Selected terms will be listed below

this step is optional

Please prepare the long-range interaction data according to the format specification Learn more ↗

interaction data file URL

The index file must be accessible from the same path
If interaction data file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

Display mode

Selected terms will be listed below

this step is optional

BAM files are no longer supported, use SAM files instead (tabix indexed). Learn more ↗

SAM file URL

The index file must be accessible from the same path
If bed file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

Display mode

Selected terms will be listed below

this step is optional

Beware that displaying sam file over large genomic region may overload our server, and increases the risk of crashing your computer

DataHub accomodates tracks of all types, along with metadata annotation

Hub descriptor file format ↗

Available custom tracks by file type

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Heatmap track (0)

Genome annotation track (0)

Long range interaction track (0)

Read alignment track (0)

Click delete button to permanently remove a custom track

Your custom tracks in an organized way

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Row	Column

Metadata vocabulary

The metadata is used to annotate heatmap tracks.
Check the checkbox to display the term in metadata color map.

Manage scaffold sequence

Determine which scaffold sequences (chromosomes, contigs, etc) shall be displayed and in what order of appearance.

TO ADD: click "Add more" button;
TO REMOVE: click ✕ and mark for removal, click again to cancel;
TO MOVE: click on a row to select a sequence, and move with ▲ ▼ buttons;

click "Update" to finalize any change.

Customize browser display

Miscellaneous functions

The space on the left of genome heatmap

This space contains correlation coefficient plots and track names, adjust width to get suitable view
min: 100 pixels max: 300 pixels default: 110 pixels

Get data in genome heatmap

links to files will be here

Data will be retrieved for all tracks in genome heatmap, over currently displayed region

Get genomic DNA sequence

link to file will be here

e.g. chr10:23860171-23860260 chromosome name, start, stop can be separated by space/tab/dash/colon

If coordinate is specified, will retrieve sequence over given region; else, will retrieve sequence for currently displayed region. Allowed sequence length retricted under 1,000,000 basepairs.

Gene Plot

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0 - Enter genes

	Enter a list of gene names or coordinates
	Display gene body for genes no effect for genomic coordinates genebody txstart 2500 0

1 - Select a quantitative track

NONE selected NONE NONE

2 - Choose graph type

Quartiles & extremes

All genes and genomic intervals are tiled together, genes are always from 5' to 3', relative to their strands. Track data of each gene are summarized into fixed length vectors, and median value over each data point is plotted.

Number of data points

Line width median curve image width height
other curves use lighter color
plot average values

Spaghetti

Number of data points

Line width line color image width height

Gene parts

Profiles of gene parts (3 kb promoter, 5' UTR, exons, introns, 3' UTR) will be plotted as separate curves, in the same fashion as first plot type (only applies to genes, genomic coordinates will be skipped)

Number of data points for each segment type

Line width image width height

promoter 5' UTR exons introns 3' UTR

Above colors are for median curves. Lighter color will be used for other curves. whisker range outlier ?
plot average values

Clustering

Run hierarchical or K-means clustering analysis on genes, and explore result through its interactive features.

Number of data points

Clustering method

distance metric agglomeration number of clusters

Row height plot width of data points
use global min/max positive value negative value (white for zero baseline)

3 - Choose rendering method

- R software generates box plots in form of still PNG images
- Google Chart generates interative line plots

You don't need to make selection for this type of graph

Firefox user: after first time using this function, the image is probably not updating anymore. This is because your browser is doing a too good job caching stuff. Follow this note to turn off caching so you can see the image updating.
If you don't see the image after clicking 'Make plot' button, it's likely that you're running into 'URL too long' problem. Try reducing number of genes and/or number of data points and do again.

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GO BACK

Get data

genes with 0 standard deviation are excluded from clustering analysis

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⚙

Relocate

Configure

positive value ≥ threshold

negative value ≤ threshold

	automatic scale
	fixed scale
	min: max:
	percentile threshold: 90 in case outlier values screw up the view
	« ‹ ↓ › »

	log transform
	log2 ln log10

P-value cutoff:
cutoff line color

pixels

apply to all tracks

Configure

Font	family: bold
	size: text color

item color

items with positive score

items with negative score

Item color:
forward reverse mismatch

Select heatmap track

Select custom track

Heatmap tracks to be added

Track detail

General

Data processing

Other versions

GEO

Read alignment

Information

Editing metadata for

No metadata annotation.
Click button to annotate.

Metadata annotation

** message console **

	Quick help display tips over various components
♞	Relocation jump to another place in genome
	Sticky note make a sticky note
	Bird's Eye View Whole-genome snapshot
	Gene Plot focus on a set of genes
	High-quality Browser shot for your publication and manuscripts

3 kb promoter and gene body
3 kb promoter	gene body
5' UTR	3' UTR
custom region...



upstream: 2500 bp	downstream: 0 bp
Define origin: transcription start site transcription stop site entire gene body