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

Table 5 Over-represented gene categories in some regression patterns from EASE functional analysis.

Reg. Patterns	Gene Category	List Hits	List Total	Pop. Hits	Pop. Total	EASE Score
LD	Cell adhesion	10	64	52	699	3.53E-02
LU	Immune regulation
	defense response	43	159	98	699	9.77E-07
	response to biotic stimulus	44	159	104	699	2.38E-06
	immune response	37	159	88	699	2.77E-05
	response to external stimulus	50	159	142	699	1.79E-04
	immune cell activation	5	159	6	699	2.58E-02
	cell activation	5	159	6	699	2.58E-02
	lymphocyte activation	5	159	6	699	2.58E-02
	B-cell activation	4	159	4	699	3.79E-02
	Other biological functions	18	159	43	699	7.52E-03
QLCD	Coenzyme and prosthetic group metabolism	7	139	12	699	1.73E-02
QLCU	Signaling
	cyclic-nucleotide-mediated signaling	3	12	4	699	1.33E-03
	second-messenger-mediated signaling	3	12	5	699	2.20E-03
	G-protein signaling, coupled to cyclic nucleotide second messenger	2	12	3	699	4.65E-02
	cAMP-mediated signaling	2	12	3	699	4.65E-02
	Protein metabolism	7	12	173	699	3.16E-02
QLVU	Immune regulation
	response to pest/pathogen/parasite	21	98	61	699	5.80E-05
	response to wounding	14	98	40	699	1.54E-03
	inflammatory response	12	98	32	699	2.19E-03
	innate immune response	12	98	32	699	2.19E-03
	defense response	24	98	98	699	3.88E-03
	response to biotic stimulus	25	98	104	699	3.98E-03
	immune response	22	98	88	699	4.82E-03
	response to stress	23	98	98	699	8.67E-03
	response to chemical substance	7	98	18	699	2.80E-02
	humoral defense mechanism (sensu Vertebrata)	6	98	14	699	3.32E-02
	response to external stimulus	28	98	142	699	3.53E-02
	Cell surface receptor linked signal transduction	18	98	80	699	3.64E-02
	Cell-matrix adhesion	4	98	6	699	3.78E-02

"Reg. Patterns" stands for the regression patterns identified by the proposed regression method; 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 (770) that are contained in EASE database, the remaining 71 genes do not have a biological function identified by EASE; "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 regression pattern; "List Hits" stands for the number of genes in "List Total" that are classified into each gene category.

ISSN: 1471-2105