IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Formulating and testing hypotheses in functional genomics
Artificial Intelligence in Medicine
TreeHugger: A New Test for Enrichment of Gene Ontology Terms
INFORMS Journal on Computing
Journal of Biomedical Informatics
Gene set analysis using principal components
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Bi-k-bi clustering: mining large scale gene expression data using two-level biclustering
International Journal of Data Mining and Bioinformatics
A hypothesis test for equality of bayesian network models
EURASIP Journal on Bioinformatics and Systems Biology
Sensitive detection of pathway perturbations in cancers: extended abstract
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
A high-dimensional two-sample test for the mean using random subspaces
Computational Statistics & Data Analysis
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Motivation: In high-throughput genomic and proteomic experiments, investigators monitor expression across a set of experimental conditions. To gain an understanding of broader biological phenomena, researchers have until recently been limited to post hoc analyses of significant gene lists. Method: We describe a general framework, significance analysis of function and expression (SAFE), for conducting valid tests of gene categories ab initio. SAFE is a two-stage, permutation-based method that can be applied to various experimental designs, accounts for the unknown correlation among genes and enables permutation-based estimation of error rates. Results: The utility and flexibility of SAFE is illustrated with a microarray dataset of human lung carcinomas and gene categories based on Gene Ontology and the Protein Family database. Significant gene categories were observed in comparisons of (1) tumor versus normal tissue, (2) multiple tumor subtypes and (3) survival times. Availability: Code to implement SAFE in the statistical package R is available from the authors. Contact:fwright@bios.unc.edu; wbarry@bios.unc.edu; nobel@email.unc.edu Supplementary information: http://www.bios.unc.edu/~fwright/SAFE