Assessment of gene order computing methods for Alzheimer's disease.
BACKGROUND
Computational genomics of Alzheimer disease (AD), the most common form of senile dementia, is a nascent field in AD research. The field includes AD gene clustering by computing gene order which generates higher quality gene clustering patterns than most other clustering methods. However, there are few available gene order computing methods such as Genetic Algorithm (GA) and Ant Colony Optimization (ACO). Further, their performance in gene order computation using AD microarray data is not known. We thus set forth to evaluate the performances of current gene order computing methods with different distance formulas, and to identify additional features associated with gene order computation.


METHODS
Using different distance formulas- Pearson distance and Euclidean distance, the squared Euclidean distance, and other conditions, gene orders were calculated by ACO and GA (including standard GA and improved GA) methods, respectively. The qualities of the gene orders were compared, and new features from the calculated gene orders were identified.


RESULTS
Compared to the GA methods tested in this study, ACO fits the AD microarray data the best when calculating gene order. In addition, the following features were revealed: different distance formulas generated a different quality of gene order, and the commonly used Pearson distance was not the best distance formula when used with both GA and ACO methods for AD microarray data.


CONCLUSIONS
Compared with Pearson distance and Euclidean distance, the squared Euclidean distance generated the best quality gene order computed by GA and ACO methods.
College of Management Science, Chengdu University of Technology, Chengdu 610059, China.
Benqiong
B
Hu
Gang
G
Jiang
Chaoyang
C
Pang
Shipeng
S
Wang
Qingzhong
Q
Liu
Zhongxue
Z
Chen
Charles R
CR
Vanderburg
Jack T
JT
Rogers
Youping
Y
Deng
Xudong
X
Huang
D000465:Algorithms; D000544:Alzheimer Disease / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D023061:Gene Order; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis