A scalable method for integration and functional analysis of multiple microarray datasets

• Published in: Bioinformatics 2006-12, Vol.22 (23), p.2890-2897
• Main Authors: Huttenhower, Curtis, Hibbs, Matt, Myers, Chad, Troyanskaya, Olga G.
• Format: Article
• Language: English
• Subjects: Algorithms; Bayes Theorem; Biological and medical sciences; Databases, Genetic; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; General aspects; Information Storage and Retrieval - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Saccharomyces cerevisiae; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Systems Integration
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl492

Motivation: The diverse microarray datasets that have become available over the past several years represent a rich opportunity and challenge for biological data mining. Many supervised and unsupervised methods have been developed for the analysis of individual microarray datasets. However, integrated analysis of multiple datasets can provide a broader insight into genetic regulation of specific biological pathways under a variety of conditions. Results: To aid in the analysis of such large compendia of microarray experiments, we present Microarray Experiment Functional Integration Technology (MEFIT), a scalable Bayesian framework for predicting functional relationships from integrated microarray datasets. Furthermore, MEFIT predicts these functional relationships within the context of specific biological processes. All results are provided in the context of one or more specific biological functions, which can be provided by a biologist or drawn automatically from catalogs such as the Gene Ontology (GO). Using MEFIT, we integrated 40 Saccharomyces cerevisiae microarray datasets spanning 712 unique conditions. In tests based on 110 biological functions drawn from the GO biological process ontology, MEFIT provided a 5% or greater performance increase for 54 functions, with a 5% or more decrease in performance in only two functions. Contact:[e-mail] Supplementary information: Supplementary data, a collection of predictions made by MEFIT and software implementing MEFIT are available online at .