Improvement in reliability of probabilistic test of significant differences in GeneChip experiments.
A probabilistic test (FUMI theory) for GeneChip experiments has been proposed for selecting the genes which show significant differences in the gene expression levels between a single pair of treatment and control. This paper describes that the reliability of the judgment by the FUMI theory can be enhanced, when the selected genes are referred to biomolecular-functional networks of a commercial database. The genes judged as being differently expressed are grouped into a cluster in the biomolecular networks. It is also demonstrated that false positive genes have a trend in the networks to be isolated from each other, and also away from the clustered genes, since the false positive genes are randomly selected.
Toda
Kyoko
K
National Institute of Health Sciences, 1-18-1 Kami-Yoga, Setagaya, Tokyo 158-8501, Japan.
Ishida
Seiichi
S
Nakata
Kotoko
K
Matsuda
Rieko
R
Shigemoto-Mogami
Yukari
Y
Ozawa
Shogo
S
Sawada
Jun-ichi
J
Ohno
Yasuo
Y
Inoue
Kazuhide
K
Shudo
Koichi
K
Hayashi
Yuzuru
Y
D000465:Algorithms; D030562:Databases, Protein; D004791:Enzyme Inhibitors / Q000494:pharmacology; D018922:HL-60 Cells; D006801:Humans; D015233:Models, Statistical; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D011493:Protein Kinase C / Q000037:antagonists & inhibitors; D015203:Reproducibility of Results; D013755:Tetradecanoylphorbol Acetate
D004791:Enzyme Inhibitors; D011493:Protein Kinase C; D013755:Tetradecanoylphorbol Acetate