ERA

Download the full-sized PDF of Making Gene Sets More CoherentDownload the full-sized PDF

Analytics

Share

Permanent link (DOI): https://doi.org/10.7939/R3T959

Download

Export to: EndNote  |  Zotero  |  Mendeley

Communities

This file is in the following communities:

Graduate Studies and Research, Faculty of

Collections

This file is in the following collections:

Theses and Dissertations

Making Gene Sets More Coherent Open Access

Descriptions

Other title
Subject/Keyword
Correlation (Statistics)
DNA microarrays
Genes
Type of item
Thesis
Degree grantor
University of Alberta
Author or creator
Mahdavifard, Fariba
Supervisor and department
Russ Greiner, Department of Computing Science
Examining committee member and department
Guohui Lin , Department of Computing Science
Paul Stothard, Department of Agricultural, Food and Nutritional Science (AFNS)
Department
Department of Computing Science
Specialization

Date accepted
2009-10-06T16:06:09Z
Graduation date
2009-11
Degree
Master of Science
Degree level
Master's
Abstract
One important goal in microarray data analysis is to learn a predictor using a patient’s microarray data to predict some important characteristics of that patient. The high dimensionality of data makes learning such classifiers very challenging. We tried to use prior biological knowledge to tackle the challenges. Our colleagues have produced clusters of genes with a common function, called “PBT”s, for mouse and human. We hoped we could use each cluster as a single feature. This is most effective if each PBT is “coherent”. They expect all PBTs to be coherent; but while mouse PBTs are coherent, human PBTs are not. In this thesis we propose a method, called MkCoh, to improve the coherency of each PBT by removing and flipping some genes. We expected the predictors based on the revised PBTs to be more accurate than the ones based on either the original PBTs, or on the original gene expression values. However, our experimental results did not demonstrate this; we explored some possible reasons.
Language
English
DOI
doi:10.7939/R3T959
Rights
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication

File Details

Date Uploaded
Date Modified
2014-04-25T00:07:51.278+00:00
Audit Status
Audits have not yet been run on this file.
Characterization
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 1006450
Last modified: 2015:10:12 12:23:30-06:00
Filename: Mahdavifard_Fariba_Fall2009.pdf
Original checksum: a7f2f54060cf628b79abe3d49ae72509
Well formed: true
Valid: true
Page count: 77
Activity of users you follow
User Activity Date