Lin, Yuefeng
(2014)
Towards the Construction of a Transcriptional Landscape of the Human Genome: Data Analysis and Data Compression.
Master's Thesis, University of Pittsburgh.
(Unpublished)
This is the latest version of this item.
Abstract
In the thesis, we built a genome-wide polyadenylation map with sequencing data sets from various human tissues and cell lines. With the map, we analyzed the pattern and distribution of polyadenylation sites in human genome. And we explored the differential polyadenylation patterns of non-coding and novel genes. Meanwhile, we have created the Expression and Polyadenylation Database (xPAD) as a web portal for the polyadenylation map. Moreover, we revealed the regulatory marks that might correlated with polyadenylation sites we have found.
Besides, we unveiled a novel group of small YB-1 associated RNAs and investigate their possible regulation mechanism where we found multiple transcription factors and histone modification may mark the location of YB-1 associated RNA.
We also implemented an Assembly-based Sequencing data Encoding Tool, AbSEnT. With this tool, we exhibited the feasibility and efficiency of the novel assembly-based compression algorithm by achieving a higher compression ratio than general-purpose compression tools. Meanwhile, we investigated the distribution of word frequency in sequencing data and found it shares a similarity with natural languages we used. If the connection could be proved, we may borrow the knowledge and experience from what we have learned in the research of natural language into the analysis of sequencing data.
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Details
| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
|
| ETD Committee: |
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| Date: |
28 October 2014 |
| Date Type: |
Publication |
| Defense Date: |
28 August 2014 |
| Approval Date: |
28 October 2014 |
| Submission Date: |
28 October 2014 |
| Access Restriction: |
No restriction; Release the ETD for access worldwide immediately. |
| Number of Pages: |
131 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
School of Medicine > Computational and Systems Biology |
| Degree: |
MS - Master of Science |
| Thesis Type: |
Master's Thesis |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
Sequencing data analysis, alternative polyadenylation, Assembly-based seqeuncing data compression, small RNAs |
| Date Deposited: |
28 Oct 2014 13:36 |
| Last Modified: |
15 Nov 2016 14:25 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/23424 |
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Towards the Construction of a Transcriptional Landscape of the Human Genome: Data Analysis and Data Compression. (deposited 28 Oct 2014 13:36)
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