Whole genome regulatory variant evaluation for transcription factor binding
Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2015
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| Online Access: | http://hdl.handle.net/1721.1/99829 |
| _version_ | 1826191289198051328 |
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| author | Zeng, Haoyang, Ph.D. Massachusetts Institute of Technology |
| author2 | David K. Gifford. |
| author_facet | David K. Gifford. Zeng, Haoyang, Ph.D. Massachusetts Institute of Technology |
| author_sort | Zeng, Haoyang, Ph.D. Massachusetts Institute of Technology |
| collection | MIT |
| description | Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015. |
| first_indexed | 2024-09-23T08:53:33Z |
| format | Thesis |
| id | mit-1721.1/99829 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T08:53:33Z |
| publishDate | 2015 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/998292020-03-31T17:58:12Z Whole genome regulatory variant evaluation for transcription factor binding Whole genome WAVE for TF binding Zeng, Haoyang, Ph.D. Massachusetts Institute of Technology David K. Gifford. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Electrical Engineering and Computer Science. Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015. Cataloged from PDF version of thesis. Includes bibliographical references (pages 41-44). With the advent of high-throughput sequencing technology, Genome Wide Association Studies (GWAS) have identified thousands of genetic variants that are associated with disease and complex traits. Many of these variants reside in the non-coding region of the genome, and affect gene expression and downstream cellular phenotype by disrupting the regulatory machinery of the cell. For example these variants can alter the binding of the transcription factors (TF). In this thesis we present Whole-genome regulAtory Variant Evaluation (WAVE), a computational method that models the TF binding ChIP-seq signal solely from DNA sequence and predicts genetic a variant's effect on TF binding. Applying WAVE to two important transcription factors, NFnB and CTCF, we show that WAVE accurately predicts ChIP-seq signal on held-out chromosome. WAVE discovers the DNA motif of the target TF as well as the binding co-factors, displaying substantially greater expressiveness in modeling TF binding than conventional motif-based approaches. Furthermore, with AUC larger than 0.7 in the most stringent control scenario, WAVE outperformed existing motif-based approaches in predicting genetic variants associated with allele-specific binding. by Haoyang Zeng. S.M. 2015-11-09T19:51:33Z 2015-11-09T19:51:33Z 2015 2015 Thesis http://hdl.handle.net/1721.1/99829 927347507 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 44 pages application/pdf Massachusetts Institute of Technology |
| spellingShingle | Electrical Engineering and Computer Science. Zeng, Haoyang, Ph.D. Massachusetts Institute of Technology Whole genome regulatory variant evaluation for transcription factor binding |
| title | Whole genome regulatory variant evaluation for transcription factor binding |
| title_full | Whole genome regulatory variant evaluation for transcription factor binding |
| title_fullStr | Whole genome regulatory variant evaluation for transcription factor binding |
| title_full_unstemmed | Whole genome regulatory variant evaluation for transcription factor binding |
| title_short | Whole genome regulatory variant evaluation for transcription factor binding |
| title_sort | whole genome regulatory variant evaluation for transcription factor binding |
| topic | Electrical Engineering and Computer Science. |
| url | http://hdl.handle.net/1721.1/99829 |
| work_keys_str_mv | AT zenghaoyangphdmassachusettsinstituteoftechnology wholegenomeregulatoryvariantevaluationfortranscriptionfactorbinding AT zenghaoyangphdmassachusettsinstituteoftechnology wholegenomewavefortfbinding |