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Unformatted text preview: 1 1 Introduction to Gene Set Testing Peng Liu 4/17/2008 2 What we have tested for microarray data ¡ So far for the tests we have learned (2-sample t-test, moderated t-test, SAM test, etc), we are testing each individual genes to find a list (or a rank) for the differentially expressed ones. ¡ These tests are useful in detecting individual genes but has limitations. 3 Some limitations of individual testing ¡ If we have moderate changes in gene expression, we might not be able to detect any significance after controlling the multiple testing error. ¡ Sometimes, the result might be a long list of significant genes. It is difficult to interpret the results. ¡ We might have information about functional categories of genes, individual testing does not make any use of those information. 4 Gene Set Testing ¡ Alternatively, we might want to look at sets of genes and check whether a set has interesting behavior for the microarray experiment. ¡ This problem has been referred to as “gene set enrichment analysis”, “significance analysis of functional categories” or just simply “testing sets of genes”. 2 5 Gene Sets ¡ The gene sets are defined based on prior knowledge from biology, such as genes from known metabolic pathways or genes sharing same transcription factor binding sites. ¡ These knowledge is organized in networks of functional categories; genes are annotated to the same category by virtue of a shared biological property. 6 Databases for Annotations ¡ There are databases that provide biological annotations for known genes, such as Gene Ontology (GO) Protein Families (Pfam) Swiss-Prot Kyoto Encyclopedia of Genes and Genomes (KEGG) 7 Gene Ontology (GO) ¡ GO terms provide one example of information that is...
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This note was uploaded on 08/27/2009 for the course STAT 447 taught by Professor Staff during the Spring '08 term at Iowa State.
- Spring '08