What's new? what's certain? - scoring search results in the presence of overlapping data sources
DILS'07 Proceedings of the 4th international conference on Data integration in the life sciences
Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis
International Journal of Data Mining and Bioinformatics
Explaining genetic knock-out effects using cost-based abduction
IJCAI'11 Proceedings of the Twenty-Second international joint conference on Artificial Intelligence - Volume Volume Two
On a meaningful exploitation of machine and human reasoning to tackle data-intensive decision making
Intelligent Decision Technologies
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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: ogt@cs.princeton.edu Supplementary information: Supplementary data, a collection of predictions made by MEFIT and software implementing MEFIT are available online at http://function.princeton.edu/mefit/.