Computational investigation of DNA methylation and C2H2 zinc finger transcription factor binding
Abstract/Contents
- Abstract
- DNA binding regulatory proteins known as transcription factors (TFs) and biochemical modifications to DNA such as DNA methylation play a key role in regulating gene activity. In my thesis, I develop computational methods for leveraging novel datasets to gain insight into how these processes affect gene regulation. I first describe a new method for finding genetic differences that are associated with variation of DNA methylation across individuals. I then describe methods for revealing the DNA binding preferences of one of the most ubiquitous but poorly understood class of TFs known as C2H2 zinc finger TFs. I present a case study in which I train and interpret deep convolutional neural networks to reveal how mutations in CTCF, an important C2H2 zinc finger TF, affect its binding preferences.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2017 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Kaplow, Irene Miriam |
|---|---|
| Associated with | Stanford University, Computer Science Department. |
| Primary advisor | Fraser, Hunter B |
| Primary advisor | Kundaje, Anshul, 1980- |
| Thesis advisor | Fraser, Hunter B |
| Thesis advisor | Kundaje, Anshul, 1980- |
| Thesis advisor | Bejerano, Gill, 1970- |
| Thesis advisor | Snyder, Michael, Ph. D |
| Advisor | Bejerano, Gill, 1970- |
| Advisor | Snyder, Michael, Ph. D |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Irene Miriam Kaplow. |
|---|---|
| Note | Submitted to the Department of Computer Science. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2017. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2017 by Irene Miriam Kaplow
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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