Identifying new genes involved in the DNA damage checkpoint pathway Courtney Onodera March 16, 2005.

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