Table 2

EASE analysis of proteomics and SAGE data

Proteomics*

SAGE


Manually determined theme

Transmembrane

Mitochondrial genes

Top EASE theme

Transmembrane (SWISS-PROT keyword)

Mitochondrion (chromosome)


*Themes of proteins predicted to have transmembrane domains versus all proteins in a brain homogenate. Themes of SAGE tags identified in human platelets versus all human genes in LocusLink. The predicted 454 transmembrane proteins in a proteomics study by Wu et al. [25] were analyzed with the categorical over-representation function of EASE for enriched themes with respect to the total of 1,610 proteins identified in a crude brain homogenate. Similarly, the SAGE tags detected by Gnatenko et al. [26] in a SAGE-based study of human platelets were analyzed for enriched themes against a background of all human genes in LocusLink. In both cases the manually determined theme is compared to the most significant EASE category as determined by EASE score. The categorical system from which the category derives is shown in parentheses.

Hosack et al. Genome Biology 2003 4:R70   doi:10.1186/gb-2003-4-10-r70

Open Data