Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments

Table 6 Over-represented gene categories in some k-means clusters from EASE functional analysis.

K-means Clusters	Gene Category	List Hits	List Total	Pop. Hits	Pop. Total	EASE Score
K2	Immune Regulation
	immune response	23	121	88	699	3.02E-02
	defense response	25	121	98	699	3.02E-02
	response to biotic stimulus	26	121	104	699	3.38E-02
K4	Humoral immune regulation	5	37	24	699	3.01E-02
K5	Immune Regulation
	immune response	18	80	88	699	1.25E-02
	response to biotic stimulus	20	80	104	699	1.51E-02
	defense response	19	80	98	699	1.72E-02
	Cell death
	apoptosis	9	80	34	699	2.91E-02
	programmed cell death	9	80	35	699	3.43E-02
	Ion Homeostasis
	ion homeostasis	5	80	13	699	4.88E-02
	cell ion homeostasis	5	80	13	699	4.88E-02
	Embryogenesis and morphogenesis	4	80	6	699	2.16E-02
	Other biological functions	12	80	43	699	5.39E-03
K6	Immune Regulation
	innate immune response	14	87	32	699	3.03E-05
	inflammatory response	14	87	32	699	3.03E-05
	response to pest/pathogen/parasite	20	87	61	699	3.32E-05
	response to wounding	15	87	40	699	1.04E-04
	defense response	24	87	98	699	6.22E-04
	response to biotic stimulus	24	87	104	699	1.57E-03
	immune response	21	87	88	699	2.41E-03
	response to stress	22	87	98	699	4.07E-03
	response to chemical substance	7	87	18	699	1.59E-02
	acute-phase response	4	87	6	699	2.73E-02
	chemotaxis	6	87	16	699	3.65E-02
	taxis	6	87	16	699	3.65E-02
	response to external stimulus	25	87	142	699	4.55E-02
	Regulation
	regulation of biological process	11	87	39	699	1.45E-02
	regulation of cellular process	11	87	39	699	1.45E-02
	regulation of cell proliferation	9	87	30	699	2.25E-02
	Cell surface receptor linked signal transduction	17	87	80	699	2.50E-02

In the "Gene Category" column, the gene categories are further summarized to broader categories (in bold); "Pop. Total" stands for the number of total input genes that are contained in EASE database; "Pop. Hits" stands for the number of genes in "Pop. Total" that are classified into each gene category; "List Total" stands for the number of genes in "Pop. Total" that are classified into each k-means cluster; "List Hits" stands for the number of genes in "List Total" that are classified into each gene category.

ISSN: 1471-2105