MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

Table 1 Numbers of genes used in the MAPPFinder calculations

	FVB benchmark dataset for development
Genes measured	9,946
Genes linked to MGD directly	6,267
Genes linked to MGD via UniGene	220
Genes linked to GO terms	5,120
Unique genes linked to GO	4,574
Genes measured/associated in GO process	3,544/4,962 (71.4%)
Genes measured/associated in GO component	3,238/4,691 (69.0%)
Genes measured/associated in GO function	3,999/5,846 (68.4%)
	12.5-day embryo
	Increased	Decreased
Genes changed	2,219	1,775
Genes linked to GO process	806	711
Genes linked to GO component	726	657
Genes linked to GO function	885	783

Of the 9,946 genes measured by this array, 6,267 were linked to the MGD database via the GenBank accession numbers referenced by MGD. An additional 220 genes were linked to MGD using UniGene as an intermediate step (see Materials and methods). Of these 6,487 genes, 5,120 were found in the mouse GO gene-association files. Once duplicate probes were removed, 4,574 unique genes were used for the MAPPFinder analysis. This dataset comprised 71.4% of the 4,962 genes associated with GO process terms, 69% of the 4,691 genes associated with GO component terms, and 68.4% of the 5,846 genes associated with GO function terms [15]. In the 12.5-day embryo, 2,219 genes met the criterion for increased gene expression, 806 having process annotation, 726 having component annotation, and 885 having function annotation. The decreased criterion found 1,775 genes, 711 in process, 657 in component, and 783 in function.

ISSN: 1474-760X