A constraint optimization framework for discovery of cellular signaling and regulatory networks
Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2011
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| Online Access: | http://hdl.handle.net/1721.1/65772 |
| _version_ | 1811095993717882880 |
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| author | Huang, Shao-shan Carol |
| author2 | Ernest Fraenkel. |
| author_facet | Ernest Fraenkel. Huang, Shao-shan Carol |
| author_sort | Huang, Shao-shan Carol |
| collection | MIT |
| description | Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011. |
| first_indexed | 2024-09-23T16:36:38Z |
| format | Thesis |
| id | mit-1721.1/65772 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T16:36:38Z |
| publishDate | 2011 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/657722019-04-12T14:39:39Z A constraint optimization framework for discovery of cellular signaling and regulatory networks Huang, Shao-shan Carol Ernest Fraenkel. Massachusetts Institute of Technology. Computational and Systems Biology Program. Massachusetts Institute of Technology. Computational and Systems Biology Program. Computational and Systems Biology Program. Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011. Cataloged from PDF version of thesis. Includes bibliographical references. Cellular signaling and regulatory networks underlie fundamental biological processes such as growth, differentiation, and response to the environment. Although there are now various high-throughput methods for studying these processes, knowledge of them remains fragmentary. Typically, the majority of hits identified by transcriptional, proteomic, and genetic assays lie outside of the expected pathways. In addition, not all components in the regulatory networks can be exposed in one experiment because of systematic biases in the assays. These unexpected and hidden components of the cellular response are often the most interesting, because they can provide new insights into biological processes and potentially reveal new therapeutic approaches. However, they are also the most difficult to interpret. We present a technique, based on the Steiner tree problem, that uses a probabilistic protein-protein interaction network and high confidence measurement and prediction of protein-DNA interactions, to determine how these hits are organized into functionally coherent pathways, revealing many components of the cellular response that are not readily apparent in the original data. We report the results of applying this method to (1) phosphoproteomic and transcriptional data from the pheromone response in yeast, and (2) phosphoproteomic, DNaseI hypersensitivity sequencing and mRNA profiling data from the U87MG glioblastoma cell lines over-expressing the variant III mutant of the epidermal growth factor receptor (EGFRvIII). In both cases the method identifies changes in diverse cellular processes that extend far beyond the expected pathways. Analysis of the EGFRVIII network connectivity property and transcriptional regulators that link observed changes in protein phosphorylation and differential expression suggest a few intriguing hypotheses that may lead to improved therapeutic strategy for glioblastoma. by Shao-shan Carol Huang. Ph.D. 2011-09-13T17:50:40Z 2011-09-13T17:50:40Z 2011 2011 Thesis http://hdl.handle.net/1721.1/65772 749445561 eng M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 135 p. application/pdf Massachusetts Institute of Technology |
| spellingShingle | Computational and Systems Biology Program. Huang, Shao-shan Carol A constraint optimization framework for discovery of cellular signaling and regulatory networks |
| title | A constraint optimization framework for discovery of cellular signaling and regulatory networks |
| title_full | A constraint optimization framework for discovery of cellular signaling and regulatory networks |
| title_fullStr | A constraint optimization framework for discovery of cellular signaling and regulatory networks |
| title_full_unstemmed | A constraint optimization framework for discovery of cellular signaling and regulatory networks |
| title_short | A constraint optimization framework for discovery of cellular signaling and regulatory networks |
| title_sort | constraint optimization framework for discovery of cellular signaling and regulatory networks |
| topic | Computational and Systems Biology Program. |
| url | http://hdl.handle.net/1721.1/65772 |
| work_keys_str_mv | AT huangshaoshancarol aconstraintoptimizationframeworkfordiscoveryofcellularsignalingandregulatorynetworks AT huangshaoshancarol constraintoptimizationframeworkfordiscoveryofcellularsignalingandregulatorynetworks |