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| Full Citation |
| Material Information |
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Title: |
Leveraging Gene Networks to Estimate Perturbations on Gene Expression |
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Series Title: |
CISE Technical Reports |
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Physical Description: |
Technical Reports |
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Creator: |
Nirmalya Bandyopadhyay
Manas Somaiya
Tamer Kahveci
Sanjay Ranka |
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Publisher: |
Computer and Information Science and Engineering, University of Florida |
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Publication Date: |
2010 |
| Notes |
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Abstract: |
External factors such as radiation, drugs or chemotherapy can
alter the expressions of a set of genes. We call these genes the
primarily affected genes. Primarily affected genes can in time change
the expressions of other genes as they activate/suppress each other
through interactions. Measuring the gene expressions before and
after applying an external factor (i.e., perturbations) in microarray
experiments can reveal how the expression of each gene changes.
It however can not tell the cause of the change.
In this paper, we consider the problem of identifying primarily
affected genes given the expression measurements of a set of genes
before and after the application of an external perturbation. We
develop a new probabilistic method to quantify the cause of differential
expression of each gene. Our method considers the possible gene
interactions in regulatory and signaling networks, for a large number
of perturbations. It uses a Bayesian model with the help of Markov
Random Fields to capture the dependency between the genes. It
also provides the underlying distribution of the impact with confidence
interval.
Our experiments on both real and synthetic datasets demonstrate
that our method can find primarily affected genes with high accuracy.
In our experiments, our method was 100% accurate when the
difference between expected expressions of primarily and secondarily
affected genes is at least half of the standard deviation of the
gene expressions. Our experiments also suggest that our method
is significantly more accurate then SSEM, a recent relevant method,
and the Studet’s t-test. |
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Funding: |
Support for the development of the technical infrastructure and partner training provided by the United States Department of Education TICFIA program. |
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Acquisition: |
Collected for University of Florida's Institutional Repository by the UFIR Self-Submittal tool. Submitted by Dina Benson. |
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Publication Status: |
Published |
| Record Information |
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Bibliographic ID: |
IR00000079 |
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Volume ID: |
VID00001 |
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Source Institution: |
University of Florida Institutional Repository |
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Rights Management: |
Permissions granted to the University of Florida Institutional Repository and University of Florida Digital Collections to allow use by the submitter. All rights reserved by the source institution. |
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