title: The characterisation of three types of genes that overlie copy number variable regions.
abstract: BACKGROUND
  Due to the increased accuracy of Copy Number Variable region (CNV) break point mapping, it is now possible to say with a reasonable degree of confidence whether a gene (i) falls entirely within a CNV; (ii) overlaps the CNV or (iii) actually contains the CNV. We classify these as type I, II and III CNV genes respectively.
  
  
  RESULTS
  Here we show that although type I genes vary in copy number along with the CNV, most of these type I genes have the same expression levels as wild type copy numbers of the gene. These genes must, therefore, be under homeostatic dosage compensation control. Looking into possible mechanisms for the regulation of gene expression we found that type I genes have a significant paucity of genes regulated by miRNAs and are not significantly enriched for monoallelically expressed genes. Type III genes, on the other hand, have a significant excess of genes regulated by miRNAs and are enriched for genes that are monoallelically expressed.
  
  
  CONCLUSIONS
  Many diseases and genomic disorders are associated with CNVs so a better understanding of the different ways genes are associated with normal CNVs will help focus on candidate genes in genome wide association studies.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. cara@sanger.ac.uk
authors.forename: Cara
authors.initials: C
authors.lastname: Woodwark
authors.forename: Alex
authors.initials: A
authors.lastname: Bateman
mesh_terms: D000483:Alleles; D016000:Cluster Analysis; D056915:DNA Copy Number Variations / Q000235:genetics*; D005786:Gene Expression Regulation; D005796:Genes / Q000235:genetics*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D012984:Software
chemical_list: D035683:MicroRNAs