Journal of Biomedical Informatics
Biological pathways as features for microarray data classification
Proceedings of the 2nd international workshop on Data and text mining in bioinformatics
Formulating and testing hypotheses in functional genomics
Artificial Intelligence in Medicine
PReMI '09 Proceedings of the 3rd International Conference on Pattern Recognition and Machine Intelligence
PReMI '09 Proceedings of the 3rd International Conference on Pattern Recognition and Machine Intelligence
Mining patterns in disease classification forests
Journal of Biomedical Informatics
International Journal of Data Mining and Bioinformatics
GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Classifying Very High-Dimensional Data with Random Forests Built from Small Subspaces
International Journal of Data Warehousing and Mining
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Motivation: Although numerous methods have been developed to better capture biological information from microarray data, commonly used single gene-based methods neglect interactions among genes and leave room for other novel approaches. For example, most classification and regression methods for microarray data are based on the whole set of genes and have not made use of pathway information. Pathway-based analysis in microarray studies may lead to more informative and relevant knowledge for biological researchers. Results: In this paper, we describe a pathway-based classification and regression method using Random Forests to analyze gene expression data. The proposed methods allow researchers to rank important pathways from externally available databases, discover important genes, find pathway-based outlying cases and make full use of a continuous outcome variable in the regression setting. We also compared Random Forests with other machine learning methods using several datasets and found that Random Forests classification error rates were either the lowest or the second-lowest. By combining pathway information and novel statistical methods, this procedure represents a promising computational strategy in dissecting pathways and can provide biological insight into the study of microarray data. Availability: Source code written in R is available from http://bioinformatics.med.yale.edu/pathway-analysis/rf.htm Contact: hongyu.zhao@yale.edu Supplementary Information: Supplementary Data are available at http://bioinformatics.med.yale.edu/pathway-analysis/rf.htm