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A panoptic approach to studying microRNA expression in breast tumors

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TitleInfo
Title
A panoptic approach to studying microRNA expression in breast tumors
Name (type = personal)
NamePart (type = family)
Bhatt
NamePart (type = given)
Priyanka
NamePart (type = date)
1987-
DisplayForm
Priyanka Bhatt
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Srinivasan
NamePart (type = given)
Shankar
DisplayForm
Shankar Srinivasan
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
Haque
NamePart (type = given)
Syed
DisplayForm
Syed Haque
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Mital
NamePart (type = given)
Dinesh
DisplayForm
Dinesh Mital
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Shibata
NamePart (type = given)
Masayuki
DisplayForm
Masayuki Shibata
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Fenyo
NamePart (type = given)
David
DisplayForm
David Fenyo
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
School of Health Professions
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2014
DateOther (qualifier = exact); (type = degree)
2014-10
CopyrightDate (encoding = w3cdtf)
2014
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
Breast cancer is the second leading cause of cancer related death amongst women and has a major impact on the lives of those affected by it. Previous research has uncovered that miRNAs, a type non-coding RNA, play a key role in the onset and development of breast tumors. Genomics, transcriptomics and proteomics studies have shed light on the intricate involvement of miRNA in mediating breast cancer progression. These small molecules are involved in many biological processes and we have yet to understand all the levels of complexity. Studying miRNA can lead to more efficient methods of screening and treatment for breast tumors while providing us with other key information from the molecular level. As confirmed by previous studies, miRNAs are good candidates for diagnostic as well as prognostic markers. This project takes a panoptic approach to studying miRNA in breast cancer genomics and proteomics and will strive to accomplish the following goals: Visualize miRNA expression data through heatmaps and identify sub-types. - We hypothesize that we will see a difference in expression of miRNAs across subtypes. Use heatmaps to examine miRNA expression across race. - We hypothesize that miRNA expression will vary across race. Perform PCA to deduce potential miRNA biomarkers for each subtype of breast cancer. - We hypothesize that we will find at least one unique biomarker for each subtype of breast cancer. Find the top 20 miRNA pairs with statistically significant correlation in expression. - We hypothesize that these pairs will have miRNAs from the same family. Study networks and pathways. - We hypothesize that we will find networks within subtypes of breast cancer. We also feel that miRNAs will be involved in more than one disease pathway. Data from The Cancer Genome Atlas (TCGA) data portal, which is an open source data portal open to the public, was utilized for the purposes of this project. The data is generated through miRNA-sequencing techniques with the aid of an Illumina Genome Analyzer. We used a combination of self-generated scripts in Perl and R and web based databases to filter, sort and analyze our data [1, 2]. On visual interpretation of our heatmaps we found different patterns of miRNA expression in the various sub-types of breast cancer. Patterns across race were not as significantly different upon visual interpretation but this may be attributed to data from a small cohort. Our PCA revealed potential biomarkers for each subtype of breast cancer. We suggest hsa-mir-127 and hsa-mir-379 as potential biomarkers of the basal subtype, hsa-mir-19a, hsa-mir126, hsa-mir-20a and hsa-mir-30a as potential biomarkers of the HER2 subtype, hsa-mir-222 as a potential biomarker of the Luminal A subtype and hsa-mir-152, hsa-mir-26b and hsa-mir-200c as potential biomarkers of the Luminal B subtype. By graphing these potential biomarkers across all subtypes we have visually confirmed our findings. We found 20 pairs of miRNAs with statistically significant correlation in expression and of those 6 were pairs that with miRNAs that are not related. We found miRNA-gene networks within two subtypes of breast cancer and generated a schematic to show the first layer of interaction. We used an online tool to generate another schematic that illuminates miRNA involvement in various pathways. We feel that our study has led to some interesting findings. We encourage future studies to further validate our proposed biomarkers as well as improve our methods. Our study lacked data from normal tissue samples; the inclusion of which we feel would have yielded more thorough results. In conclusion, we believe that computational methods of data analysis in studying miRNA expression data are truly powerful and the results of these methods will only get more accurate as more data is made available.
Subject (authority = RUETD)
Topic
Biomedical Informatics
Subject (authority = ETD-LCSH)
Topic
RNA
Subject (authority = ETD-LCSH)
Topic
Breast--Cancer--Treatment
Subject (authority = ETD-LCSH)
Topic
Biochemical markers
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
RelatedItem (type = host)
TitleInfo
Title
School of Health Related Professions ETD Collection
Identifier (type = local)
rucore10007400001
Identifier
ETD_5894
Identifier (type = doi)
doi:10.7282/T3319XHP
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (xv, 119 p. : ill.)
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Note (type = statement of responsibility)
by Priyanka Bhatt
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Genre (authority = ExL-Esploro)
ETD doctoral
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Bhatt
GivenName
Priyanka
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2014-09-24 14:33:09
AssociatedEntity
Name
Priyanka Bhatt
Role
Copyright holder
Affiliation
Rutgers University. School of Health Related Professions
AssociatedObject
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.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Technical

RULTechMD (ID = TECHNICAL1)
ContentModel
ETD
OperatingSystem (VERSION = 5.1)
windows xp
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