A probabilistic generative model for GO enrichment analysis Export

@article{citeulike:3196937, abstract = {The Gene Ontology (GO) is extensively used to analyze all types of high-throughput experiments. However, researchers still face several challenges when using GO and other functional annotation databases. One problem is the large number of multiple hypotheses that are being tested for each study. In addition, categories often overlap with both direct parents/descendents and other distant categories in the hierarchical structure. This makes it hard to determine if the identified significant categories represent different functional outcomes or rather a redundant view of the same biological processes. To overcome these problems we developed a generative probabilistic model which identifies a (small) subset of categories that, together, explain the selected gene set. Our model accommodates noise and errors in the selected gene set and GO. Using controlled GO data our method correctly recovered most of the selected categories, leading to dramatic improvements over current methods for GO analysis. When used with microarray expression data and ChIP-chip data from yeast and human our method was able to correctly identify both general and specific enriched categories which were overlooked by other methods. 10.1093/nar/gkn434}, author = {Lu, Yong and Rosenfeld, Roni and Simon, Itamar and Nau, Gerard J. and Bar-Joseph, Ziv}, citeulike-article-id = {3196937}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn434}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/36/17/e109}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18676451}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18676451}, day = {1}, doi = {10.1093/nar/gkn434}, journal = {Nucl. Acids Res.}, keywords = {enrichment, gene\_ontology}, month = {August}, pages = {gkn434+}, posted-at = {2008-09-05 10:29:03}, priority = {4}, title = {A probabilistic generative model for GO enrichment analysis}, url = {http://dx.doi.org/10.1093/nar/gkn434}, year = {2008} }

TY - JOUR ID - citeulike:3196937 L3 - citeulike-article-id:3196937 N2 - The Gene Ontology (GO) is extensively used to analyze all types of high-throughput experiments. However, researchers still face several challenges when using GO and other functional annotation databases. One problem is the large number of multiple hypotheses that are being tested for each study. In addition, categories often overlap with both direct parents/descendents and other distant categories in the hierarchical structure. This makes it hard to determine if the identified significant categories represent different functional outcomes or rather a redundant view of the same biological processes. To overcome these problems we developed a generative probabilistic model which identifies a (small) subset of categories that, together, explain the selected gene set. Our model accommodates noise and errors in the selected gene set and GO. Using controlled GO data our method correctly recovered most of the selected categories, leading to dramatic improvements over current methods for GO analysis. When used with microarray expression data and ChIP-chip data from yeast and human our method was able to correctly identify both general and specific enriched categories which were overlooked by other methods. 10.1093/nar/gkn434 JF - Nucl. Acids Res. TI - A probabilistic generative model for GO enrichment analysis SP - gkn434 KW - enrichment KW - gene_ontology AU - Lu, Yong AU - Rosenfeld, Roni AU - Simon, Itamar AU - Nau, Gerard AU - Bar-Joseph, Ziv PY - 2008/08/01/ UR - http://dx.doi.org/10.1093/nar/gkn434 ER -