Statistical Analysis of mRNA-miRNA Interaction A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at George Mason University by Surajit Bhattacharya Master of Sciences George Mason University, 2012 Director: Daniel N. Cox, Associate Professor School of Systems Biology Spring Semester 2013 George Mason University Fairfax, VA This work is licensed under a creative commons attribution-noderivs 3.0 unported license. ii DEDICATION I dedicate this to all my teachers from whom I have learned a lot and am still in the process of learning more. iii ACKNOWLEDGEMENTS I would like to thank my parents, my wife, friends, relatives, and supporters who have made this happen. I really would like to thank Dan Veltri, for his immense help in the computational aspect of the project and Srividya Chandramouli for helping me understand the biological aspect of the problem. I would also like to thank Jaimin Patel for helping me out with the database management and UI aspect of the Project. I would also like to thank Dr. Anand Vidyashankar, Dr. Larry Tang and Dr. Daniel Cox for the immense help in the project. iv TABLE OF CONTENTS List of Figures .................................................................................................................... vi List of Equations .............................................................................................................. viii List of Abbreviations ......................................................................................................... ix Abstract ............................................................................................................................... x Introduction ......................................................................................................................... 1 Material and Methods ......................................................................................................... 7 Results ............................................................................................................................... 12 Figures............................................................................................................................... 15 Discussion ......................................................................................................................... 25 Conclusion ........................................................................................................................ 30 Future WoRK .................................................................................................................... 31 Appendix-I (Codes) .......................................................................................................... 32 Index .................................................................................. Error! Bookmark not defined. References ......................................................................................................................... 61 Curriculum Vitae .............................................................................................................. 63 v LIST OF FIGURES FIGURE 1: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-990 (MIRNA PROBE ID 144103_AT) AND SIM (MRNA PROBE ID 143508_AT). THE STATISTICAL TESTS ARE BROWNIAN (RED COLOR IN THE LEGEND), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y-AXIS REPRESENTS THE RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK CALCULATED FOR A SINGLE MIRNA-MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN A SINGLE EXPERIMENT. THE X-AXIS REPRESENTS ALL MICROARRAY EXPERIMENTS AVAILABLE FOR D. MELANOGASTER IN THE GEO DATABASE. THIS PAIR IS ALSO PREDICTED IN THE 3 TARGET PREDICTION DATABASES FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA. ............................................................................................................. 15 FIGURE 2: GPROFILER WEB TOOL IS USED TO FETCH THE MRNA NAME FOR A GIVEN PROBE ID. .......................................... 16 FIGURE 3: IDENTIFICATION OF THE INTRAGENIC MIRNAS, FOR A GIVEN MRNA USING THE INTRAGENIC LIST. ........................ 16 FIGURE 4: FINDING THE CORRESPONDING TARGET MRNAS FOR THE MIRNA USING OUR MIAMI WEB TOOL. A DATABASE SEARCH IS MADE ACROSS THE THREE DATABASES (PITA, TARGETSCAN AND MIRANDA). ......................................... 17 FIGURE 5: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-990 (PROBE ID-144103) AND LSP2 (PROBE ID-143239). THE 3 TESTS ARE BROWNIAN (RED), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y AXIS IS RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK (WITH RESPECT TO THE CORRELATION), FOR A SINGLE MIRNA- MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN AN EXPERIMENT. THE X-AXIS REPRESENTS ALL THE EXPERIMENTS FOR D. MELANOGASTER IN THE GEO DATABASE. THIS MIRNA-TARGET PAIR WAS NOT FOUND IN THE 3 TARGET PREDICTION FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA. ............................................... 18 FIGURE 6: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-959 (MIRNA PROBE ID 151413_AT) AND MBL (MRNA PROBE ID 147360_AT). THE STATISTICAL TESTS ARE BROWNIAN (RED), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y-AXIS REPRESENTS THE RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK CALCULATED FOR A SINGLE MIRNA-MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN A SINGLE EXPERIMENT. THE X-AXIS REPRESENTS ALL MICROARRAY EXPERIMENTS AVAILABLE FOR D. MELANOGASTER IN THE GEO DATABASE. THIS PAIR IS ALSO PREDICTED IN THE 3 TARGET PREDICTION DATABASES FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA. ............................................................................................................................................................. 19 FIGURE 7: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-959 (MIRNA PROBE ID 151413_AT) AND RPL26 (MRNA PROBE ID 149019_AT). THE STATISTICAL TESTS ARE BROWNIAN (RED), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y-AXIS REPRESENTS THE RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK CALCULATED FOR A SINGLE MIRNA-MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN A SINGLE EXPERIMENT. THE X-AXIS REPRESENTS ALL MICROARRAY EXPERIMENTS AVAILABLE FOR D. MELANOGASTER IN THE GEO DATABASE. THIS PAIR IS NOT PREDICTED IN THE 3 TARGET PREDICTION DATABASES FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA. ..... 20 FIGURE 8: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-984 (MIRNA PROBE ID 144476_AT) AND CG31530 (MRNA PROBE ID 149292_AT). THE STATISTICAL TESTS ARE BROWNIAN (RED), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y-AXIS REPRESENTS THE RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK CALCULATED FOR A SINGLE MIRNA-MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN A SINGLE EXPERIMENT. THE X-AXIS REPRESENTS ALL MICROARRAY EXPERIMENTS AVAILABLE FOR D. MELANOGASTER IN THE GEO DATABASE. THIS PAIR IS PREDICTED IN THE 3 TARGET PREDICTION DATABASES FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA. ..... 21 FIGURE 9: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-984 (MIRNA PROBE ID 144476_AT) AND CG8661 (MRNA PROBE ID 145243_AT). THE STATISTICAL TESTS ARE BROWNIAN (RED), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y-AXIS REPRESENTS THE RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK CALCULATED FOR A SINGLE MIRNA-MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN A SINGLE EXPERIMENT. THE X-AXIS vi REPRESENTS ALL MICROARRAY EXPERIMENTS AVAILABLE FOR D. MELANOGASTER IN THE GEO DATABASE. THIS PAIR IS NOT PREDICTED IN THE 3 TARGET PREDICTION DATABASES FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA. ..... 22 FIGURE 10: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-990 (MIRNA PROBE ID 144103_AT) AND PLEXA (MRNA PROBE ID 153857_AT). THE STATISTICAL TESTS ARE BROWNIAN (RED), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y-AXIS REPRESENTS THE RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK CALCULATED FOR A SINGLE MIRNA-MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN A SINGLE EXPERIMENT. THE X-AXIS REPRESENTS ALL MICROARRAY EXPERIMENTS AVAILABLE FOR D. MELANOGASTER IN THE GEO DATABASE. THIS PAIR IS PREDICTED IN THE 3 TARGET PREDICTION DATABASES FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA. ..... 23 FIGURE 11: GRAPHICAL REPRESENTATION OF 3 STATISTICAL TESTS BETWEEN DME-MIR-984 (MIRNA PROBE ID 144476_AT) AND LECTIN-21CB (MRNA PROBE ID 145542_AT). THE STATISTICAL TESTS ARE BROWNIAN (RED), DISTANCE (GREEN) AND PEARSON (BLUE). THE Y-AXIS REPRESENTS THE RANKING PERCENTILE, WHICH IS THE PERCENTILE RANK CALCULATED FOR A SINGLE MIRNA-MRNA PAIR IN COMPARISON TO ALL OTHER MIRNA-MRNA PAIRS IN A SINGLE EXPERIMENT. THE X-AXIS REPRESENTS ALL MICROARRAY EXPERIMENTS AVAILABLE FOR D. MELANOGASTER IN THE GEO DATABASE. THIS PAIR IS NOT PREDICTED IN THE 3 TARGET PREDICTION DATABASES FOR MIRNA-MRNA VIZ. TARGETSCAN, MIRANDA AND PITA ............................................................................................................................................................. 24 vii LIST OF EQUATIONS Equation Page EQUATION 1 FORMULA FOR THE PEARSON CORRELATION (COURTESY: WIKIPEDIA.COM) .................................................... 8 EQUATION 2. DISTANCE CORRELATION (COURTESY: WIKIPEDIA.COM) ........................................................................... 10 viii LIST OF ABBREVIATIONS GEO-Gene Expression Omnibus mRNA- Messenger RNA miRNA- micro RNA. ix ABSTRACT STATISTICAL ANALYSIS OF MRNA-MIRNA INTERACTION Surajit Bhattacharya, MS George Mason