title: Coexpression analysis of human genes across many microarray data sets.
abstract: We present a large-scale analysis of mRNA coexpression based on 60 large human data sets containing a total of 3924 microarrays. We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in multiple data sets, establishing a high-confidence network of 8805 genes connected by 220,649 "coexpression links" that are observed in at least three data sets. Confirmed positive correlations between genes were much more common than confirmed negative correlations. We show that confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes. Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function.
authors.affiliation: Columbia Genome Center, Columbia University, New York, New York 10032, USA.
authors.forename: Homin K
authors.initials: HK
authors.lastname: Lee
authors.forename: Amy K
authors.initials: AK
authors.lastname: Hsu
authors.forename: Jon
authors.initials: J
authors.lastname: Sajdak
authors.forename: Jie
authors.initials: J
authors.lastname: Qin
authors.forename: Paul
authors.initials: P
authors.lastname: Pavlidis
mesh_terms: D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D005786:Gene Expression Regulation / Q000235:genetics*; D005796:Genes / Q000235:genetics*; D008040:Genetic Linkage / Q000235:genetics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*