title: The CO-Regulation Database (CORD): a tool to identify coordinately expressed genes.
abstract: BACKGROUND
  Meta-analysis of gene expression array databases has the potential to reveal information about gene function. The identification of gene-gene interactions may be inferred from gene expression information but such meta-analysis is often limited to a single microarray platform. To address this limitation, we developed a gene-centered approach to analyze differential expression across thousands of gene expression experiments and created the CO-Regulation Database (CORD) to determine which genes are correlated with a queried gene.
  
  
  RESULTS
  Using the GEO and ArrayExpress database, we analyzed over 120,000 group by group experiments from gene microarrays to determine the correlating genes for over 30,000 different genes or hypothesized genes. CORD output data is presented for sample queries with focus on genes with well-known interaction networks including p16 (CDKN2A), vimentin (VIM), MyoD (MYOD1). CDKN2A, VIM, and MYOD1 all displayed gene correlations consistent with known interacting genes.
  
  
  CONCLUSIONS
  We developed a facile, web-enabled program to determine gene-gene correlations across different gene expression microarray platforms. Using well-characterized genes, we illustrate how CORD's identification of co-expressed genes contributes to a better understanding a gene's potential function. The website is found at http://cord-db.org.
authors.affiliation: Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: John P
authors.initials: JP
authors.lastname: Fahrenbach
authors.affiliation: Center for Research Informatics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Jorge
authors.initials: J
authors.lastname: Andrade
authors.affiliation: Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America; Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: McNally
mesh_terms: D051358:Cyclin-Dependent Kinase 4 / Q000235:genetics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D019942:Genes, p16; D006801:Humans; D017570:MyoD Protein / Q000235:genetics / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D059467:Transcriptome; D014746:Vimentin / Q000235:genetics / Q000378:metabolism
chemical_list: D017570:MyoD Protein; C057363:MyoD1 myogenic differentiation protein; D014746:Vimentin; C495900:CDK4 protein, human; D051358:Cyclin-Dependent Kinase 4