Transcript ppt
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