Affiliations: Biobase Corporation, 100 Cummings Center, Ste. 420B,
Beverly, MA 01915, USA | Department of Biochemistry, Boston University School
of Medicine, Boston, MA 02118, USA | Department of Genetics, Stanford University School of
Medicine, Stanford, CA 94305, USA
Abstract: Microarray technology has resulted in an explosion of complex,
valuable data. Integrating data analysis tools with a comprehensive underlying
database would allow efficient identification of common properties among
differentially regulated genes. In this study we sought to compare the utility
of various databases in microarray analysis. The Proteome
BioKnowledge® Library (BKL), a manually
curated, proteome-wide compilation of the scientific literature, was used to
generate a list of Gene Ontology (GO) Biological Process (BP) terms enriched
among proteins involved in cardiovascular disease. Analysis of DNA microarray
data generated in a study of rat vascular smooth muscle cell responses revealed
significant enrichment in a number of GO BPs that were also enriched among
cardiovascular disease-related proteins. Using annotation from LocusLink and
chip annotation from the Gene Expression Omnibus yielded fewer enriched
cardiovascular disease-associated GO BP terms. Data sets of orthologous genes
from mouse and human were generated using the BKL Retriever. Analysis of these
sets focusing on BKL Disease annotation, revealed a significant association of
these genes with cardiovascular disease. These results and the extensive
presence of experimental evidence for BKL GO and Disease features, underscore
the benefits of using this database for microarray analysis.
Keywords: Microarray analysis, gene ontology, disease, cardiovascular disease, protein databases
