1. Learning of Synthetic Lethal Interactions in Yeast

2. ROD at CISBAN

Yeast High-Throughput experiments on ageing

Semi-automated

Robot Object Database to track strains through multiple experiments

3. Synthetic Lethality

Telomere uncapping

• CDC13-1

Double deletions

Drug interactions

Can we predict it?

4. Friends and Enemies Network

Implement paper:

• Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS. Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res. 2008 Dec;18(12):1991-2004.

5. Friends and Enemies 6. Gas Diffusion Network 7. Gas Diffusion Networks ij == ji i j 8. Gas Diffusion Networks 9. 1 1 2 3 4 5 2 3 3 4 5 5 Gas Diffusion Networks 10. 1 1 2 3 4 5 2 3 3 4 5 5 Same pathway? 11. 1 1 2 3 4 5 2 3 3 4 5 5 Same pathway? 12. 1 1 2 3 4 5 2 3 3 4 5 5 Different pathways? 13. 1 1 2 3 4 5 2 3 3 4 5 5 Different pathways? 14. 1 1 2 3 4 5 2 3 3 4 5 5 Different Pathways? 15. 16. Kernel Methods

Similar to Support Vector Machines

Compare all nodes to all other nodes and assign a numerical comparison

In this case, the reachability from each node to every other node in the graph

17. Some squiggles

G- : the reachability using odd length paths

G+ : the reachability of even length paths

G is the reachability of all path lengths

18. Experimental confirmation

Gene: ADA2

• Transcriptional co-activator in histone acetylation

Used G- with synthetic lethal and synthetic sick from BioGRID

Additional known positives may be found further down the ranked list

19. 20. True Positives 21. False Positives - Orange 22. False Negatives 23. Results

48 True Positives

52 False Positives

45 False Negatives

• 12 not in BioGRID

24. Re-implementation

BioGrid 2.0.27

• Total yeast interactions:

• • Them: 18 492

• • Me: 18 505

• Yeast interactions after removing duplicates and singletons

• • Them: 13 022

• • Me: 13 913

Used their query gene ADA2

25. Problems

Some genes had different names

No hits!

Email to author: Please check your methods and try again

26. Future Work

Given up on paper

Could be potential in gas diffusion methods

• Cedric's resistance-based method

• Possible collaboration with Daniel Ashlock