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Potts model clustering for discovering patterns of epigenetic marks
Descriptive
TypeOfResource
Text
TitleInfo
(ID = T-1)
Title
Potts model clustering for discovering patterns of epigenetic marks
Identifier
ETD_3073
Identifier
(type = hdl)
http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000057612
Language
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(authority = ISO639-2);
(type = code)
eng
Genre
(authority = marcgt)
theses
Subject
(ID = SBJ-1);
(authority = RUETD)
Topic
Physics and Astronomy
Subject
(ID = SBJ-2);
(authority = ETD-LCSH)
Topic
Epigenesis--Research
Subject
(ID = SBJ-3);
(authority = ETD-LCSH)
Topic
Histones
Subject
(ID = SBJ-4);
(authority = ETD-LCSH)
Topic
Cluster analysis
Abstract
(type = abstract)
Study of epigenetics leads to understanding of the regulation of gene expression not caused by the changes in the underlying DNA sequences. This area of biological research has drawn much interest as large amounts of epigenetic data from numerous experiments were generated in recent past. In this thesis, we use the Potts model clustering method, which is based on statistical mechanics, to discover patterns in histone modification data. After a general overview of the epigenome and an introduction to common methods of clustering, we discuss why we need special cluster analysis methods for the data at hand. Then, we introduce our tool of choice, namely, the superparamagnetic Potts clustering method. We discuss the Potts model and the Swendsen-Wang method of Monte Carlo simulation, which avoids the usual slowing down experienced near phase transition. We apply Potts model clustering to histone modification data in highly conserved regions to discover the patterns of epigenetic marks and compare them with background reading. We also contrast the results from our method with that from usual Kmeans clustering approach. Finally, we discuss the biological significance of our computational results.
PhysicalDescription
Form
(authority = gmd)
electronic resource
Extent
x, 64 p. : ill.
InternetMediaType
application/pdf
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text/xml
Note
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Ph.D.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = vita)
Includes vita
Note
(type = statement of responsibility)
by Junyi Li
Name
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Li
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Junyi
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1980-
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author
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Junyi Li
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Sengupta
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Anirvan
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chair
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Advisory Committee
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Anirvan Sengupta
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(type = personal)
NamePart
(type = family)
Bartynski
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(type = given)
Robert
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internal member
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Advisory Committee
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Robert Bartynski
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(ID = NAME-4);
(type = personal)
NamePart
(type = family)
Sellwood
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(type = given)
Jerry
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internal member
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Advisory Committee
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Jerry Sellwood
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(ID = NAME-5);
(type = personal)
NamePart
(type = family)
Bhanot
NamePart
(type = given)
Gyan
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internal member
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Advisory Committee
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Gyan Bhanot
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NamePart
(type = family)
Pirrotta
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Vincenzo
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outside member
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Advisory Committee
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Vincenzo Pirrotta
Name
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NamePart
Rutgers University
Role
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(authority = RULIB)
degree grantor
Name
(ID = NAME-2);
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NamePart
Graduate School - New Brunswick
Role
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(authority = RULIB)
school
OriginInfo
DateCreated
(qualifier = exact)
2011
DateOther
(qualifier = exact);
(type = degree)
2011-01
Place
PlaceTerm
(type = code)
xx
RelatedItem
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TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
(type = RULIB)
ETD
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
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rucore19991600001
Location
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(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T3FQ9W84
Genre
(authority = ExL-Esploro)
ETD doctoral
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Rights
RightsDeclaration
(AUTHORITY = GS);
(ID = rulibRdec0006)
The author owns the copyright to this work.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
RightsHolder
(ID = PRH-1);
(type = personal)
Name
FamilyName
Li
GivenName
Junyi
Role
Copyright Holder
RightsEvent
(ID = RE-1);
(AUTHORITY = rulib)
Type
Permission or license
DateTime
2010-12-22 13:36:24
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(AUTHORITY = rulib)
Role
Copyright holder
Name
Junyi Li
Affiliation
Rutgers University. Graduate School - New Brunswick
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Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
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Technical
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ETD
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application/pdf
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application/x-tar
FileSize
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2836480
Checksum
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