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

0.1

0.2

0.3

0.4

0.5

0.6

0.00E+00

1.00E-05

2.00E-05

3.00E-05

4.00E-05

5.00E-05

6.00E-05

7.00E-05

8.00E-05

9.00E-05

1.00E-04

P-Value

Sen

sit

ivit

y Known+Camptothecin+HydroxyureaKnown+CamptothecinKnown+HydroxyureaCamptothecin+HydroxyureaKnown DNA Damage-onlyCamptothecin-onlyHydroxyurea-onlyMSGR combined query

Precision of Combined Methods by P-Value

0

0.05

0.1

0.15

0.2

0.25

0.00E+00

1.00E-05

2.00E-05

3.00E-05

4.00E-05

5.00E-05

6.00E-05

7.00E-05

8.00E-05

9.00E-05

1.00E-04

P-Value

Pre

cis

ion

Known+Camptothecin+Hydroxyurea

Known+Camptothecin

Known+Hydroxyurea

Camptothecin+Hydroxyurea

Known DNA Damage-only

Camptothecin-only

Hydroxyurea-only

MSGR combined query

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