Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation

Table 1 Clustering and CLASSIFI results for data from 3 ligands

GO ID	g	f	c	n	expt	prob	GO type	GO term	Cluster ID	anti-CD40	LPS	AIG
GO:0005634	2490	254	380	64	38.76	8.71E-06	CC	Nucleus	1	1	1	1
GO:0009058	2490	141	180	25	10.19	1.36E-05	BP	biosynthesis	2	1	1
GO:0008372	2490	1409	1	1	0.566	5.66E-01	CC	CC unknown	3	1	-1	-1
GO:0046072	2490	2	160	2	0.129	4.10E-03	BP	dTDP metabolism	4	1		1
GO:0009605	2490	30	3	2	0.036	4.18E-04	BP	response to external stimulus	5	1		-1
GO:0016655	2490	14	331	11	1.861	4.94E-08	MF	oxidoreductase activity, acting on NADH	6	1
GO:0005773	2490	12	11	4	0.053	1.00E-07	CC	Vacuole	7	-1	-1	1
GO:0003779	2490	15	277	9	1.669	6.30E-06	MF	actin binding	8	-1	-1	-1
GO:0016758	2490	6	245	4	0.59	1.17E-03	MF	Transferase activity, transferring hexosyl groups	9	-1	-1
GO:0006417	2490	2	4	1	0.003	3.21E-03	BP	regulation of protein biosynthesis	10	-1		1
GO:0008372	2490	1409	41	32	23.2	3.30E-03	CC	CC unknown	11	-1		-1
GO:0008047	2490	10	160	3	0.643	2.23E-02	MF	enzyme activator activity	12	-1
GO:0006397	2490	19	56	4	0.427	6.92E-04	BP	mRNA processing	13		1	1
GO:0005576	2490	156	183	33	11.47	7.28E-09	CC	extracellular	14		1
GO:0046916	2490	1	4	1	0.002	1.61E-03	BP	transition metal ion homeostasis	15		-1	1
GO:0003931	2490	3	38	2	0.046	6.74E-04	MF	Rho small monomeric GTPase activity	16		-1	-1
GO:0004032	2490	3	188	3	0.227	4.24E-04	MF	aldehyde reductase activity	17		-1
GO:0015672	2490	10	191	7	0.767	1.38E-06	BP	monovalent inorganic cation transport	18			1
GO:0016892	2490	3	50	2	0.06	1.17E-03	MF	endoribonuclease activity, producing other than	19			-1

Gene clusters (Cluster ID 1–19) resulting from categorical clustering of processed data from B cells stimulated with anti-CD40, LPS, and AIG. "1" = upregulated, "-1" = downregulated, and blank = no significant change. Following CLASSIFI analysis, the GO term giving rise to the lowest probability in each gene cluster is indicated. GO ID = a unique Gene Ontology identifier assigned to a GO term that corresponds to a defined molecular function (MF), biological process (BP), or cellular component (CC). g = number of probes in the data set, f = number of probes with associated GO ID in the data set, c = number of probes in the gene cluster, n = number of probes with associated GO ID in the gene cluster. Expt = the expected number of occurrences of a given GO ID in a given cluster of size (n) based on a random distribution. Prob = the probability that the GO ID co-cluster pattern has occurred by chance.

ISSN: 1471-2105