Transcript Go to Genboree Workbench Drag your database into output box

Modules 6 and 7:
Genboree and
Epigenome Comparison
Aleksandar Milosavljevic
Epigenomics Data Analysis
and Coordination Center (EDACC)
Presented at the 2nd Epigenome Informatics Workshop
Houston, Texas, September 10th 2010
Diversity of Epigenomes
Comparing Epigenomes
Modules 3, 4, 5
Modules 6, 7
Genboree Workbench and Atlas Gene Browser
Roles
Users
Groups
Atlas Gene Browser
Access
Projects
Genome-centric
databases
Tools
Genboree Workbench
Genboree Workbench
Genboree Tools>>Workbench
Genboree Workbench
Preliminary Exercises
1. Go to Genboree Tools>>Workbench
2. Expand and shrink Data Selector tree in the Workbench
2. Examine properties in “Details” window by clicking on
objects in Data Selector
3. Read about required tool inputs and outputs by clicking on
inactive tool icons
4. Activate tool icons by selecting required Input and Output
Comparison of “broad” peaks
?
Exercise #1:
Pairwise epigenome signal comparison
Go to Genboree Workbench
Drag the following tracks into Input box:
Group: EDACC Workshop 2010
Database: EDACC Workshop 2010
Class: 0.6 HDHV_Data
Input Track: meCG:h1_bar
Input Track: meCG:imr90_bar
Class: GeneModel
Input Track: GeneModel:5’UTR
Drag your database into Output box.
Run Signal Comparison: Analysis>Epigenomics>SignalComparison
Check email for results
Two types of Genboree annotation tracks
1. HDHV (High Density - High Volume)
Example: go to Genboree Browser and select
Group: EDACC Workshop 2010
Database: EDACC Workshop 2010
Class: 0.6 HDHV_Data
Input Track: meCG:h1_bar
Input Track: meCG:imr90_bar
2. Regular tracks
Example:
Class: GeneModel
Input Track: GeneModel:5’UTR
Using attribute-values for annotations
Go to Genboree Browser
Group: EDACC Workshop 2010
Database: EDACC Workshop 2010
Class: GeneModel
Input Track: GeneModel:5’UTR
Check out many available attributes using Tabular View
Genboree Help and LFF format
Click on Genboree “Help?” button in the top right area.
Check “Help” entries.
Check out “LFF format”. View the documentation of
attribute-value pairs.
Exercise #2: Building a query
Go to Genboree Workbench
Drag your database into output box.
Build “KEGG_PATHWAY-repair-5UTR” query:
Exercise #2 (cont’d): Running a query
Running a KEGG_PATHWAY-5UTR query:
Group: Epigenome Atlas
Database: Your Database
Drag into Input Data: All Annotations in Database
and query “KEGG_PATHWAY-5UTR”
Drag into Output Targets: Your Database
Run Query
Exercise #3: Atlas similarity search
Go to Genboree Workbench
Drag the following tracks into Input Data box:
Group: Epigenomics Roadmap Repository
Database: Data Freeze 1 – Full Repo
Class: 06.HDHV Data
Input Track: SD:H1 H4Kme3
Drag your database into Output Targets box.
Run Atlas Similarity Search:
Analysis>Epigenomics>Epigenome Atlas Search
Repeat with
Input Track: H1 H3K9ac
Check email for results (results in about 1 hour)
Exercise #3 (cont’d): Atlas sim. search
Hello Aleksandar Milosavljevic,
Your searchAtlasSim tool run has completed successfully.
Job Summary:
JobID: wbJob-1283968416_700501
Input Track: SD:H1 H3K4me3
The number of targets : 247
Result Summary:
The top 10 target track matches:
Track Name Pearson correlation
SD:H1 H3K4me3
1.0
BI:iPS18c H3K4me3 2 0.8233
BI:iPS11a H3K4me3 1 0.8204
SF:H1 H3K4me3 1 0.8161
BI:ESI3 H3K9ac 2 0.816
BI:H1 H3K4me3
0.8121
SF:H1 H3K4me3 2 0.8003
BI:ESI3 H3K4me3 1 0.7998
BI:iPS15b H3K4me3 1 0.792
SD:H1 H3K4me3 3 0.7858
....
Exercise #3 (cnt’d): Atlas sim. search
Hello Aleksandar Milosavljevic,
Your searchAtlasSim tool run has completed successfully.
Job Summary:
JobID: wbJob-1284061293_073103
Input Track: SD:H1 H3K9ac
The number of targets : 247
Result Summary:
The top 10 target track matches:
Track Name Pearson correlation
SD:H1 H3K9ac
1.0
BI:H1 H3K9ac
0.8528
BI:H1 H3K9ac 1
0.846
BI:iPS15b H3K9ac 1 0.8001
BI:iPS18c H3K9ac 1 0.7698
SF:H1 H3K9ac
0.7673
BI:iPS20b H3K9ac 1 0.7449
BI:H1 H3K4me3 2 0.7351
BI:Pancreas H3K9ac 1
0.7241
BI:ESI3 H3K9ac 1 0.7086
....
Exercise #4: Atlas Gene Browser
Exercise #4: Atlas Gene Browser
Exercise #1 (continued):
Epigenome comparison
Check output track reporting results of comparison in
5’UTR methylation in IMR90 relative to H1.
Sort the track by score – note largest decrease in
IMR90 relative to H1 (largest negative score) in ODF1
Visualize output track in Genboree browser.
Search for ELF3 and visualize increase in IMR90
relative to H1.
Querying to the output of comparisons
Example: Find all repair-related genes whose 5’UTR
regions are much less methylated in IMR90 than in H1
Genboree and scripting
Everything that can be done interactively using the workbench
can also be done programmatically, typically using short scripts
in programming languages like Perl, Python, or Ruby.
This is accomplished through Genboree HTTP-based REST
APIs (Application Programming Interfaces).
Proof: the Genboree Workbench itself was written using
Genboree REST APIs.
To learn more, check Genboree Help ( under REST APIs ) – the
help is correct but incomplete -- does not document all available
functionality.
Interested to start using Genboree REST APIs? Attend Andrew
Jackson’s talk ( Module 8 )