1. PROTEIN INTERACTION NETWORK – INFERENCE TOOL DIVYA RAO CANDIDATE FOR MASTER OF SCIENCE IN BIOINFORMATICS ADVISOR: Dr. FILIPPO MENCZER CAPSTONE PROJECT PRESENTATION SCHOOL OF INFORMATICS - INDIANA UNIVERSITY April 20, 2006

2. Outline  Outline  Background  PIN-IT  Sample Results  Future Work  References  Acknowledgements Background PIN-IT Sample Results Future Work References Acknowledgements April 20, 2006 Slide 2 of 19

3. Definitions Proteins are complex, high- molecular weight organic compounds Protein interactions are associations between protein molecules Examples: enzymes, hormones, transcription factors, antibodies, structural proteins  Outline  Background  Definitions  PIN-IT  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 3 of 19

4. Experimental Approaches Immunoprecipitation  Outline  Background  Experiments  PIN-IT  Results  Future Work  References  Acknowledgements http://www.molecularstation.com/protein/immunoprecipitation/ April 20, 2006 Slide 4 of 19

5. High Throughput Experiments DNA sequence analysis –Homology & Orthology –Limited to proteins encoded by a single gene in one species or two or more genes in another  Outline  Background  Experiments  PIN-IT  Results  Future Work  References  Acknowledgements A a Species 1 Species 2 April 20, 2006 Slide 5 of 19 a b B b Species 3

6. Yeast Two Hybrid Bait & prey Transcription: DNA -> RNA Two haploid yeasts Benefit: – yeast can express genes from almost any species Limitation: –Mutations – false positives – May not detect weak or rapid interactions  Outline  Background  Experiments  PIN-IT  Results  Future Work  References  Acknowledgements http://www.biochem.arizona.edu/classes/bioc568/bioc568.htm April 20, 2006 Slide 6 of 19

7. PRISM  Outline  Background  Other Tools  PIN-IT  Results  Future Work  References  Acknowledgements http://gordion.hpc.eng.ku.edu.tr/prism/tutorial.php#predictions.php April 20, 2006 Slide 7 of 19

8. ADVICE  Background  Other Tools http://advice.i2r.a-star.edu.sg/doc/flowchart.gif April 20, 2006 Slide 8 of 19

9. Motivation Interaction maps can be used to reveal drug targets –BCL6 in humans causes B-cell non-Hodgkin lymphoma. In the fruitfly the BCL6 ortholog binds calcineurin phosphatases –Hubs vs. peripheral proteins  Outline  Background  Motivation  PIN-IT  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 9 of 19

10. Protein Interaction Network Inference Tool Infer protein-protein interactions –Known protein interactions –Protein similarity  Outline  Background  PIN-IT  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 10 of 19

11. PIN-IT Data sources Database of Interacting Proteins (DIP) Biomolecular Interaction Network Database (BIND) Proteins with GI numbers, Taxon ID & experimental source False positive rate –Immunoprecipitation, r = 0.1 –Yeast Two Hybrid, r = 0.6  Outline  Background  PIN-IT  Data Sources  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 11 of 19

12.  Outline  Background  PIN-IT  Data DIPBINDPIN-IT Number of proteins 188262780943573 Number of Interactions 541724435494659 Number of Organisms 10910201033 PIN-IT Data April 20, 2006 Slide 12 of 19

13. BLAST Basic Local Alignment Search Tool..AGTTAC.. I I I I..ACTTAG.. Smith-Waterman algorithm E-value –# of different alignments with scores equivalent to or better than S that are expected to occur in a database by chance Orthologus proteins BLASTP  Outline  Background  PIN-IT  BLAST  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 13 of 19

14. Calculating Inference A I B xy S D Where: r is the false positive rate E is the e-value from BLAST n is the size of the dataset April 20, 2006 Slide 14 of 19

15. Demo PIN-IT  Outline  Background  PIN-IT  Demo  Results  Future Work  References  Acknowledgments April 20, 2006 Slide 15 of 19

16.  Outline  Background  PIN-IT  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 16 of 19 Results 63225506324320 63237666321260 Interacts with mRNAs encoding membrane- associated proteins Putative integral membrane E3 ubiquitin ligase Putative integral membrane, negative regulation of amino acid uptake Has roles in maintenance of cell wall integrity

17. Future Work Allow for the user to upload their protein sequences and interactions Better estimation of experimental false positive rates Work with biologists to validate the tool and fine-tune the parameters  Outline  Background  PIN-IT  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 17 of 19

18. References Campbell, M. A., Heyer, L.A. Discovering Genomics, Proteomics & Bioinformatics. India: Pearson Education, 2004, pp176-183. Ito T, et al.: "A comprehensive two-hybrid analysis to explore the yeast protein interactome,". Proc Natl Acad Sci 2001, 98: 4569-74. Titz B, et al.: "What do we learn from high-throughput protein interaction data?". Expert Rev Proteomics 2004, 1: 111-21. Giot L, et al.: "A protein interaction map of Drosophila melanogaster,". Science 2003 302: 1727-1736 Aytuna,A.S, Gursoy,A. Keskin,O., (2005). Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21 (12):2850-2855 Tan, Soon-Heng, Zhang, Zhuo, Ng, See-Kiong ADVICE: Automated Detection and Validation of Interaction by Co- Evolution Nucl. Acids Res. 2004 32: W69-72 Protein Interactions by Structural Matching (PRISM): http://gordion.hpc.eng.ku.edu.tr/prism/index.php http://gordion.hpc.eng.ku.edu.tr/prism/index.php Automated Detection and Validation of Interaction by Co-Evolution (ADVICE): http://advice.i2r.a-star.edu.sg/ http://advice.i2r.a-star.edu.sg/ DIP: http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/ BIND: http://www.bind.ca/Action http://www.bind.ca/Action Immunoprecipitation Image: http://www.molecularstation.com/protein/immunoprecipitation/ http://www.molecularstation.com/protein/immunoprecipitation/ Yeast Two Hybrid system image: http://www.biochem.arizona.edu/classes/bioc568/bioc568.htm http://www.biochem.arizona.edu/classes/bioc568/bioc568.htm  Outline  Background  PIN-IT  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 18 of 19

19. Acknowledgements Dr. Filippo Menczer Dr. Haixu Tang Dr. Alessandro Flammini Dr. Sun Kim Dr. Mehmet Dalkilic Dr. Gary Wiggins Linda Hostetter  Outline  Background  PIN-IT  Results  Future Work  References  Acknowledgements April 20, 2006 Slide 19 of 19

20. Query April 20, 2006

21. Query Results

22. Node Information

23. April 20, 2006 Query Results

24. Interaction Edge Information April 20, 2006

25. Query Results

26. Similarity Edge Information April 20, 2006

27. Query Results

28. Inference Edge Information April 20, 2006