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A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes
July-September 2006 (vol. 3 no. 3)
pp. 220-231
ASCII Text
x 
 
Osman Abul, Reda Alhajj, Faruk Polat, "A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 3, pp. 220-231, July-September, 2006.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2006.29,
author = {Osman Abul and Reda Alhajj and Faruk Polat},
title = {A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {3},
number = {3},
issn = {1545-5963},
year = {2006},
pages = {220-231},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2006.29},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes
IS - 3
SN - 1545-5963
SP220
EP231
EPD - 220-231
A1 - Osman Abul,
A1 - Reda Alhajj,
A1 - Faruk Polat,
PY - 2006
KW - q-values
KW - significantly differentially expressed genes
KW - microarray
KW - pattern generation
KW - PaGE.
VL - 3
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
The problem of identifying significantly differentially expressed genes for replicated microarray experiments is accepted as significant and has been tackled by several researchers. Patterns from Gene Expression (PaGE) and q-values are two of the well-known approaches developed to handle this problem. This paper proposes a powerful approach to handle this problem. We first propose a method for estimating the prior probabilities used in the first version of the PaGE algorithm. This way, the problem definition of PaGE stays intact and we just estimate the needed prior probabilities. Our estimation method is similar to Storey's estimator without being its direct extension. Then, we modify the problem formulation to find significantly differentially expressed genes and present an efficient method for finding them. This formulation increases the power by directly incorporating Storey's estimator. We report the preliminary results on the BRCA data set to demonstrate the applicability and effectiveness of our approach.

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Index Terms:
q-values, significantly differentially expressed genes, microarray, pattern generation, PaGE.
Citation:
Osman Abul, Reda Alhajj, Faruk Polat, "A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 3, pp. 220-231, July-Sept. 2006, doi:10.1109/TCBB.2006.29
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