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Computational Analysis, Visualization and Text Mining of Metabolic Networks

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Computational Analysis, Visualization and Text Mining of Metabolic Networks COMPUTATIONAL ANALYSIS, VISUALIZATION AND TEXT MINING OF METABOLIC NETWORKS by XINJIAN QI Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Advisor: Dr. Gültekin Özsoyoğlu Department of Electrical Engineering and Computer Science CASE WESTERN RESERVE UNIVERSITY January, 2014 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of ____Xinjian Qi____________________________________________ candidate for the Doctor of Philosophy___degree *. (signed) __Dr. Gültekin Özsoyoğlu__________________________ (chair of the committee) __________Dr. Andy Podgurski______________________________ __________Dr. M. Cenk Cavusoğlu__________________________ __________Dr. Nicola Lai___________________________________ __________Dr. Z. Meral Özsoyoğlu__________________________ ___________________________________________________________ (date) _____June 24, 2013____ *We also certify that written approval has been obtained for any proprietary material contained therein. Table of Contents Table of Contents ................................................................................................................ 1 List of Tables ...................................................................................................................... 6 List of Figures ..................................................................................................................... 7 Acknowledgements ........................................................................................................... 10 Abstract ............................................................................................................................. 12 Introduction ....................................................................................................................... 14 1.1 Computational Interpretation of Metabolomics Measurements: Steady-State Metabolic Network Dynamics Analysis ....................................................................... 15 1.2 Performing Gene Lethality Testing with SMDA ............................................... 17 1.3 Visualization Tools for PathCase Systems......................................................... 19 1.4 Locating Basic Bio-Entities in Genome-Scale Reconstructed Metabolic Networks ....................................................................................................................... 22 1.5 Thesis Organization............................................................................................ 24 Computational Interpretation of Metabolomics Measurements: Steady-State Metabolic Network Dynamics Analysis ............................................................................................ 25 2.1 Introduction ........................................................................................................ 25 2.2 Condition-Based Modeling ................................................................................ 33 2.2.1 Assumptions and Terminology ................................................................... 33 2.2.2 Metabolite Pool Label Identifiers ............................................................... 36 1 2.2.3 Metabolite Label Condition Characterization ............................................. 38 2.2.4 Trigger Values and Activation Condition Sets for Reactions, Transport Processes, or Pathways ............................................................................................. 39 2.2.5 Biochemistry-Based Rules .......................................................................... 43 2.3 Active/Inactive Graph Generation And Expansion ............................................ 45 2.3.1 Initial GAI Generation ................................................................................. 46 2.3.2 GAI Graph Expansion .................................................................................. 48 2.3.3 Merging GAI Graphs ................................................................................... 56 2.3.4 Algorithm Sketch ........................................................................................ 58 2.4 Experimental Evaluation .................................................................................... 59 2.4.1 Experimental Setting ................................................................................... 59 2.4.2 Experimental Results .................................................................................. 61 2.5 Related Work: Metabolic Network Analysis Techniques .................................. 63 2.6 Conclusions ........................................................................................................ 66 Performing Gene Lethality Testing with SMDA .............................................................. 67 3.1 Introduction ........................................................................................................ 67 3.2 Summary of SMDA Algorithm .......................................................................... 70 3.2.1 SMDA Terminology ................................................................................... 70 3.2.2 Algorithm Flow ........................................................................................... 72 3.2.3 Conflicts ...................................................................................................... 74 2 3.3 Existing Gene Lethality Techniques and SMDA ............................................... 75 3.4 Revising SMDA For Gene Lethality Testing ..................................................... 80 3.5 Experimental Evaluation .................................................................................... 83 3.5.1 Experimental Setting ................................................................................... 83 3.5.2 Gene Lethality Test Results ........................................................................ 86 3.5.3 Gene Non-Lethality Test Results ................................................................ 90 3.6 Conclusions ........................................................................................................ 91 Visualization Tools for PathCase Systems ....................................................................... 92 4.1 Introduction ............................................................................................................ 92 4.2 Visualization Tool for PathCase-SB System ..................................................... 94 4.3 Visualization Tools for other PathCase Systems ............................................... 98 4.3.1 PathCase-MAW and PathCase-MAW Editor ............................................. 98 4.3.2 PathCase-SMDA ......................................................................................... 99 4.3.3 PathCase-RCMN and PathCase-Recon .................................................... 101 4.3.4 PathCase-MQL ......................................................................................... 103 4.4 General Framework .......................................................................................... 106 4.5 Visualization Tool for iPad Applications ......................................................... 108 4.6 Conclusions ...................................................................................................... 109 Locating Basic Bio-Entities in Genome-Scale Reconstructed Metabolic Networks ...... 110 5.1 Introduction ...................................................................................................... 110 3 5.1.1 Entity Identification .................................................................................. 111 5.1.2 Similarity Score ........................................................................................ 112 5.2 Metabolite Identification .................................................................................. 114 5.2.1 Exact Match via Metabolite Id/Synonyms ................................................ 116 5.2.2 Approximate Name Matching................................................................... 117 5.2.3 Filtering Metabolite Match Candidates .................................................... 125 5.3 Reaction Identification .......................................................................................... 129 5.3.1 Reaction Name Matching ......................................................................... 130 5.3.2 Reaction Property Matching ..................................................................... 131 5.3.3 Reaction Compound Matching ................................................................. 132 5.3.4 Reaction Similarity Score ......................................................................... 134 5.4 Experimental Evaluation .................................................................................. 135 5.4.1 Metabolite Identification Results .............................................................. 136 5.4.2 Reaction Identification Results ................................................................. 144 5.5 Conclusion ........................................................................................................ 150 Conclusions and Future Work ........................................................................................ 152 6.1 Future work ...................................................................................................... 153 6.1.1 SMDA ......................................................................................................
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