1. Open Day 2006 From Expression, Through Annotation, to Function Ohad Manor & Tali Goren

2. Open Day 2006 Have you ever wondered…

3. Open Day 2006 Types of Data Gene Expression (Microarray) GO Annotations Gene Expression (Microarray) GO Annotations ChIP on chip GO Annotations Gene Expression (Microarray) GO Annotations ChIP on chip Protein – Protein Interactions Sub - Cellular Localization Systematic view in genomic large scale What Characterizes these data sets?

4. Open Day 2006

5. A computational tool to check enrichment of data sets Implemented in perl Interactive command line May be scripted… Concatenate tests and matrix operations Data manipulation functions and queries What is ?

6. Open Day 2006 Using Load biological data Check enrichment of crossed data sets Extract statistically significant results Multiple hypothesis correction Cluster gene sets Save results

7. Open Day 2006 What is statistically significant? How to choose the right test to compare measurements? Paired or Unpaired? Non – Parametric: – no assumption about sample size or distribution – no parameters such as expectation or variance

8. Open Day 2006 Paired – Binary Version RAP1 Ribosome Assembly Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 RAP1 Ribosome Assembly

9. Open Day 2006 Paired – continuous version Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 heat shock Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 YPD Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 1

10. Open Day 2006 Unpaired test Gene1 Gene2 Gene4 Gene5 Gene6 heat shock Gene3 Gene7 Gene8 Gene10 heat shock 1 Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 heat shock RAP1 Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10

11. Open Day 2006 Statistics Statistics…….

12. Open Day 2006 How About Some Biology?

13. Open Day 2006 S. Cerevisiae Regulation Let’s presume we know nothing about the Yeast Use ENRICH to construct a basic regulatory network of Yeast How can we do that?

14. Open Day 2006 STE12 RAP1 YAP5 MSN2 SFP1 FHL1 GAT1 Binary values Ribosomal Stress Cell cycle Metabolism Flow chart HG test Significance threshold Ribosomal Stress Cell cycle Metabolism STE12 RAP1 YAP5 MSN2 SFP1 FHL1 GAT1 P-values Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 Ribosomal Stress Cell cycle Metabolism GO Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 ChIP STE12 RAP1 MSN2 FHL1

15. Open Day 2006 Metabolism Stress Cell cycle Yeast regulation network

16. Open Day 2006 FHL1 protein Case study

17. Open Day 2006 FHL1 – what is known Putative transcriptional regulator Predicted to be involved in stress response Required for rRNA processing Null mutant shows reduced growth rate Could we have found all of that alone?

18. Open Day 2006 Experimental various conditions genes Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 Exp. Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 FHL1 Unpaired T-test Exp.1 Exp.2 Exp.3 Exp.4 Exp.5 P-values FHL1 Exp.1 Exp.2 Exp.3 Exp.4 Exp.5 FHL1 Exp.1 Exp.2 Exp.3 Exp.4 Exp.5 Binary values Conditions HG test P-values FHL1 Heat shock AA starvation osmotic stress oxidative stress invasive growth

19. Open Day 2006 Tell me who are your friends… Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 FHL1 Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 ChIP HG test RAP1 FKH2 MBP1 GAT3 SOK2 P-values FHL1

20. Open Day 2006 Enriched conditions Growth Stress response Enriched GO annotations Ribosome assembly RAP1 SFP1 GAT3 Enriched TF’s

21. Open Day 2006 Remember this question? What is the connection between the expression level of a gene to its sub-cellular localization? Which Transcription Factors regulate Amino Acid Biosynthesis? Does a heat shock affect peripheral proteins more than it affects mitochondrial proteins? Mitochondrion Cell Periphery

22. Open Day 2006 Flow chart genes Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 Exp. Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 Gene7 Gene8 Gene9 Gene10 Localization Unpaired T-test HG test Exp.1 Exp.2 Exp.3 Exp.4 Exp.5 P-values Mitochondria Bud Neck Vacuole Cell periphery Nucleus Exp.1 Exp.2 Exp.3 Exp.4 Exp.5 Mitochondria Bud Neck Vacuole Cell periphery Nucleus Exp.1 Exp.2 Exp.3 Exp.4 Exp.5 Binary values Short HS Medium HS Long HS Severe HS Moderate HS P-values Short HS Medium HS Long HS Severe HS Moderate HS Cell periphery Mitochondria

23. Open Day 2006 Heat shock

24. Open Day 2006 Future plans Continue to develop More data available out there Build Regulation networks for the Yeast and other species

25. Open Day 2006 Questions

26. Open Day 2006 Thanks Prof. Nir Friedman Tommy Kaplan And to you for listening!!!

27. Open Day 2006