Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data

BMC Genomics

Table 2 Summary of probe remapping results using different databases

	GenBank	RefSeq	Ensembl	ZFIN	Biomart	UCSC
Probes with multiple alignments to the genome	19,585	19,585	19,585	19,585	19,585	19,585
Probes with no alignment to the genome	41,609	42,398	41,972	41,613	41,488	41,077
Probes matching multiple genes	2,718	1,674	432	2,228	1,592	1,487
Probes matching intergenic region	65,220	75,916	81,273	64,394	66,806	54,532
Probes matching intron region	8,348	6,912	9,817	9,049	10,068	10,911
< 3 probes per probe set	2,369	762	1,464	3,884	3,126	4,378
Good probes	109,903	102,505	95,209	108,999	107,087	117,782
Percentage of good probes	44.005%	41.043%	38.121%	43.643%	42.877%	47.160%
Probe sets	8,574	6,769	7,156	9,195	8,732	10,251

ISSN: 1471-2164