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.

Doniger et al. Genome Biology 2003 4:R7   doi:10.1186/gb-2003-4-1-r7

Open Data