A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

BMC Genomics

Table 3 Strain-specific differential expression in Toxoplasma gondii.

	Number of genes		Significant up- or down-regulation in:
	Total	Expressed in tachyzoites²	Any strain ( significance³)	RH (type I)	Pru (type II)	VEG (type III)	Other pattern
All genes in genome	7,793	3,986	2,078	477	570	193	838
GO-annotated genes ¹(process annotations only)	2,074	1,360	677	143	218	60	256
Gene-GO Slim mappings ¹	2,764	1,805	885	193	272	80	340
DNA metabolism	140	62 <2e-7	31 <0.01	8	7 0.03	4	12
RNA metabolism	250	177 0 .02	660 .03	16	19	4	27
Protein metabolism	806	574 <10e-6	288 <0.01	61	105 <0.01	21	101
Other metabolic process	528	331	179	31	58	14	76 0 .04
Other biological process	90	56	32	10 0.05	12	0 0.05	10
Transport	456	297	153	38	36	17	62
Signal transduction	85	54	29	7	8	3	11
Cell cycle/proliferation	52	28 0.05	13	2	5	4 0.02	2 0.04
Cell organization/biogenesis	238	151	70	16	14 0.02	10	30
Cell adhesion	17	8	2 0.05	1	0	1	0
Stress response	102	65	22 0.01	3	8	2	9
Unannotated genes	5,719	2,626	1,401	333	352	133	582

1 Multiple GO annotations are available for some genes, and some GO annotations map to multiple GO slim categories (although multiple annotations may also map to the same category). 2,074 genes include 2,979 GO annotations, corresponding to 3,503 GO Slims, for a total of 2,764 gene-GO Slim mappings.
2 Assessed using a 10% false discovery rate (see text for details).
3 Differential expression determined as described in the text. P-values represent enrichment for GO Slim terms, as determined by the hypergeometric distribution (only values less than 0.05 are shown). Green shading implies under-representation, while yellow shading implies over-representation.

ISSN: 1471-2164