We report steps toward the systematic management, standardization, and analysis 
of functional genomics data. We developed the ExpressDB database for yeast RNA 
expression data and loaded it with approximately 17.5 million pieces of data 
reported by 11 studies with three different kinds of high-throughput RNA assays. 
A web-based tool supports queries across the data from these studies. We 
examined comparability of data by converting data from 9 studies (217 
conditions) into mRNA relative abundance estimates (ERAs) and by clustering of 
conditions by ERAs. We report on generation of ERAs and condition clustering for 
non-microarray data (5 studies, 63 conditions) and describe initial attempts to 
generate microarray-based ERAs (4 studies, 154 conditions), which exhibit 
increased error, on our web site http://arep.med.harvard. edu/ExpressDB. We 
recommend standards for data reporting, suggest research into improving 
comparability of microarray data through quantifying and standardizing control 
condition RNA populations, and also suggest research into the calibration of 
different RNA assays. We introduce a model for a database that integrates 
different kinds of functional genomics data, Biomolecule Interaction, Growth and 
Expression Database (BIGED).