- Title
- A case-control approach to assess variability in distribution of distance between transcription factor binding site and transcription start site
- Creator
- Moos, Abdul Ragmaan
- ThesisAdvisor
- Machanick, Philip
- Subject
- Transcription factors
- Subject
- Proteomics
- Subject
- Chromatin
- Subject
- Chromatin immunoprecipitation
- Date
- 2017
- Type
- Thesis
- Type
- Masters
- Type
- MSc
- Identifier
- http://hdl.handle.net/10962/5315
- Identifier
- vital:20808
- Description
- Using the in-silico approach, with ENCODE ChIP-seq data for various transcription factors and different cell types; we systematically compared the distance between the transcription factor binding site (TFBS) and the transcription start (TSS). Our aim was to determine if the same transcription factor binds at a different position relative to the TSS in a normal and an abnormal cell type. We compare distribution of distance of binding sites from the TSS; to make description less verbose we call this “distance” where there is no possibility of confusion. We used a case-control methodology where the distance between the TFBS and the TSS in the normal, non-cancerous or untreated cell type is the control. The distance between the TFBS and the TSS in the cancerous or treated cell type is the case. We use the distance between the TFBS and the TSS in the control as the standard. We compared the distance between the TFBS and the TSS in the case and the control. If the distance between the TFBS and the TSS in the control was greater than the distance between the TFBS and the TSS in the case, we can infer the following. The transcription factor in the case binds closer to the TSS compared to the control. If the distance between the TFBS and the TSS in the control is smaller than the distance between the TFBS and the TSS in the case, we can infer the following. The TF in the case binds further away from the TSS compared to the control. Our method is a screening method whereby we compare ChIP-seq data to determine if there is a difference in the distribution distance between the TFBS and the TSS for normal and abnormal cell types. We used the R package ChIP-Enrich to compare the distribution of distance between ChIP-seq peak and the nearest TSS. ChIP-Enrich produces a histogram with the number of ChIP-seq peaks at a certain distance from the TSS. The results indicate for some transcription factors like GM12878-cMyc and K562-cMyc there is a difference between the distribution of distance between the TFBS and the nearest TSS. cMyc has more binding sites within a distance of 1kb from the TSS in GM12878 when compared to K562. GM12878-CTCF and K562-CTCF have slight differences when comparing their distribution of distance from the TSS. This means CTCF binds almost the same distance from the TSS in both GM12878 and K562. A549-gr treated with dexamethasone is interesting because with increase dose of dexamethasone the distribution of distance from the TSS changes as well.
- Format
- 96 pages, pdf
- Publisher
- Rhodes University, Faculty of Science, Biochemistry and Microbiology
- Language
- English
- Rights
- Moos, Abdul Ragmaan
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RU Department of Biochemistry and Microbiology (2015-)
| Thumbnail | File | Description | Size | Format | |||
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