Download Identifying new genes involved in the DNA damage checkpoint

Identifying new genes
involved in the DNA damage
checkpoint pathway
Courtney Onodera
March 16, 2005
Overview of pathway
http://biochem.wustl.edu/~burgersw3/checkpointtxt.htm
Motivation
• Lokey lab - cancer research
(therapeutics)
• Wet lab experiments:
– Knock out genes with RNAi
– Treat cells with camptothecin (DNA
damaging agent)
– See if cells proceed with cell division or not
Stuff we had to start with
• List of genes known to be involved in the DNA
damage checkpoint pathway (Scott, Josh,
and Gene Ontology)
• Chemical sensitivity data from yeast (Boone
Lab, UToronto)
– Synthetic lethal interactions with DNA damaging
agents camptothecin and hydroxyurea
– Genes ranked on scale of 0-3 (not sensitive - most
sensitive)
Strategy
• Start with a list of genes known to be involved
in the pathway
• Utilize existing recommender programs to
find additional candidates for the pathway
• Incorporate results from the different
programs along with chemical sensitivity data
to find the best overall candidates
Multi-Species Gene Recommender
(MSGR)
http://kolossus.cse.ucsc.edu:8001/GRJava/howitworks.html
Multi-species network analysis
Results were a little harder to deal with…
…leaving them out for now…
What I did
•
Ran MSGR with queries:
1. Known DNA damage checkpoint genes
2. Genes most sensitive to camptothecin
3. Genes most sensitive to hydroxyurea
•
•
Combined p-values from all tests to
get an overall p-value for each gene
Ranked all returned genes by overall
p-value
Some results…
How to tell if my results make any
sense?
• Look at known DNA-damage checkpoint
genes returned
– Rank
– Total number
• Number of knowns returned is
maximized by combining all three tests
Sensitivity of Combined Methods by P-Value
0.6
0.5
Sensitivity
0.4
Known+C amptothec in+H ydroxyurea
Known+C amptothec in
Known+H ydroxyurea
C amptothec in+H ydroxyurea
Known DN A Damage-only
C amptothec in-only
H ydroxyurea-only
M SGR c ombined query
0.3
0.2
0.1
0
0.00E+ 1.00E00
05
2.00E05
3.00E05
4.00E05
5.00E05
P-Value
6.00E05
7.00E05
8.00E05
9.00E05
1.00E04
Precision of Combined Methods by P-Value
0.25
0.2
0.15
Precision
Known+C amptothec in+H ydroxyurea
Known+C amptothec in
Known+H ydroxyurea
C amptothec in+H ydroxyurea
Known DN A Damage-only
C amptothec in-only
0.1
H ydroxyurea-only
M SGR c ombined query
0.05
0
0.00E+ 1.00E00
05
2.00E05
3.00E05
4.00E05
5.00E05
P-Value
6.00E05
7.00E05
8.00E05
9.00E05
1.00E04
Conclusion
• Combining the MSGR results from the
three queries leads to higher sensitivity
but lower precision
• Single query with known DNA damage
checkpoint genes seems to have best
combination of precision and sensitivity
Acknowledgements
•
•
•
•
Chad Chen - MSGR
Corey Powell - multi-species network
Josh Stuart
Scott Lokey