Using the Genome Browser to Explore Genomics Data

Using the Genome Browser to Explore Genomics Data
Using the Genome Browser
to Explore Genomics Data
Jean Jasinski, Ph.D.
Senior Application Scientist
Mar. 16, 2010
Features of Genome Browser
Navigation in Genome Browser
Import and Export of Information from Genome Browser
Methylation and Gene Expression Profiling of
Prostate Cancer
Methylation profiling of prostate cancer (GSE 15298)
• 20 prostate cancer tissues (Cy5); Pooled reference lymphocyte of age
matched, healthy men (Cy3)
• Agilent Human 244K CpG Island Array (treated like expression array)
Gene expression profiling of prostate cancer (GSE 3325)
• 6b
6 metastatic
t t ti prostate
t t cancer, 7 primary
t t cancer
• Affymetrix Human Genome U133 Plus 2.0 Array
Features of Genome
Flexible and Interactive Genome Browser
and values to plot
From Menu, Views > Genome Browser
Multiple experiments can be displayed in the same Genome Browser
Drag-and-drop experiment into Genome Browser
Genome Browser
Three types of objects can be plotted and viewed in Genome
•Experiment Data
– Data can be viewed for individual samples or for conditions
•Entity List
– Plot entities in list by any list-associated values (e.g., fold change, pvalues,, etc.)*
•Annotation Track
– Import and view annotation tracks in Genome Browser
*Intensity value is not a list-associated value
Plot Experiment Data in Genome Browser
Gene Expression
Genomic Copy Number
Options of values to plot depends on experiment type
Plot Entity Lists in Genome Browser
• By default, Entities in list are plotted as regions by their genomic coordinates
• T
To plot
l t Entities
E titi b
by th
i lilist-associated
i t d values
(if present):
t) Right-click
Ri ht li k > Edit
track properties > Rendering > Plot > Select Histogram, Profile, or Scatter >
Data column > Select desired column to plot
Plot Annotation Data in Genome Browser
• Annotations available on the Agilent Server include:
-Gene Track
-CpG Island Track
Transcript Track
You may also add any kind of annotation tracks that you download from an external
source such as UC Santa Cruz or with any annotation file you create.
Track Plot Options in Genome Browser
Annotation Track
Scatter Plot
Profile Plot
Region Plot
To choose data plot type: Right-click on track > Edit Track
Properties > Rendering > Plot
Track Options for Genome Browser
Right-click on track > Change track size
• Change size of selected track, all tracks, or all tracks from the same
• Fit all tracks in view
Right-click on track > Edit track properties
Rename track
Change sampling method
Apply smoothing
Show label for Entities in track
Change range of y-axis
Change plot type
And more…
Genome Browser Tool Bar
Zoom in and out
Show summary of data across
all Chromosomes in
Chromosome Selector Panel
Set order of
Import and delete
annotation tracks
User manual for
Genome Browser
Merge Selected
Reset to full
Set orientation of
tracks to horizontal or
Export image
Merge Tracks in Genome Browser
Data tracks and
annotation tracks from
same or different
Experiments can be
Copy Number Track
Log Ratio Track
Merge tracks
1 and 2
• Select multiple tracks
using Ctrl + Select
• Click on Merge icon from
Genome Browser Toolbar
p merged
g tracks,,
• To split
Right-click > Split tracks
Density View in Genome Browser
3. Entities in selected track is
displayed in Chromosome
Selector panel
2. Click on “Show
Show density in
Chromosome Selector” icon
1. Select track to view
density across all
Allows you to view all entities in selected track for all chromosomes
Example: Entity List obtained from Common Genomic Variant Regions Analysis shows regions of common variation
in Chromosome Selector panel
Navigating within
Genome Browser
GeneSpring GX 11 Genome Browser Navigation
• Jump to Chr of interest:
– Chr Selector Pane
– Drop-down menu in window
• Zoom into region of interest:
– Click drag box in Cytoband view
in Summary Panel
– Shift drag box in any data or
annotation track
• Pan
P around
d region
i off iinterest:
– Click on any track and drag
right-left with mouse
– Scroll up-down on mouse wheel
– Use right-left arrows within any
Navigation: Chromosome Selector
Select Chromosome
to view
Navigation: Chr Drop-down and Region
Enter genomic coordinate to
view region of interest
Use drop-down
drop down menu to
select Chromosome to view
Navigation: Cytoband View and Tracks
Navigate to region of interest:
• Click + drag box in Cytoband view in Summary Panel
• Shift + drag box in any data or annotation track
Navigation: Jump to Entity of Interest by Searching
in Spreadsheet of Genome Browser
Search for Entity in Spreadsheet
Spreadsheet tab displays data for selected track
h ffor Entity
E tit off interest
i t
t using
i value
l in
i any Spreadsheet
d h t columns
Entity is highlighted in Track and Spreadsheet
Double click on Entity in Spreadsheet to zoom into that Entity in Genome Browser
d h t shows
data for selected Track
Navigation: Entity List
• Entity Lists can be displayed
in Genome Browser and used
of tracks:
for navigation
– Drag-n-drop Entity List into
Genome Browser
– Scroll via right-left
arrows of
Entity List track instructs
GeneSpring GX to navigate
by jumping to next entity in
Importing and
Exporting Information
the Genome Browser
Import and Manage Tracks in Genome Browser
Click on Organism folder to 1) Delete
or add new organism and 2) Add New
build for chosen organism
Click on Build folder to 1) Delete or add
new build and 2) Delete or add track
Import Tracks for Viewing in Genome Browser
BED format is automatically
recognized in GeneSpring. Other
formats can be imported through
“Advanced Import “
Define columns to import for
custom track files
Exporting Information in Spreadsheet
Right-click on Spreadsheet:
• Export as Entity List
– Creates Entity List in Navigator containing Entities in Spreadsheet
• Export as Text
– Creates text (.tsv) file containing Spreadsheet information
Export Track Images
To export image for a single track:
Right click on track > Export as >
To export multiple tracks and Genome
Browser components: Click on
“Export Select Track as Image” icon
from Toolbar
Select tracks to export
Set Image Options for export
Folder containing exported images:
– Individual images of selected tracks
– Cytoband and Ruler of Genome Browser
– Entire view as displayed in Genome
Browser (png and html)
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