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

BMC Genomics

Table 1 Number of transcripts and genes from each database and number of alignable genes and transcripts in the UCSC genome browser

Database	No. of transcripts	No. of genes	No. of alignable transcripts	No. of alignable genes
Single data source
GenBank	59,527	36,843	25,336	14,130
RefSeq	30,499	28,999	13,304	13,172
Ensembl	35,967	25,546	35,967	25,546
Multiple data sources ¹
ZFIN	79,424	21,430	52,246	14,217
Biomart	61,047	21,322	58,135	21,322
UCSC	75,723	28,110²	75,723	28,110

¹: These databases integrate transcripts from Ensembl, RefSeq and GenBank databases.
²: Genes are defined by clustering transcripts overlapping in coding exons

ISSN: 1471-2164