title: DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.
abstract: BACKGROUND
  The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences.
  
  
  RESULTS
  Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (p<2.2e-16) than HK gene promoters. The entropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes.
  
  
  CONCLUSIONS
  Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression.
authors.affiliation: Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK.
authors.forename: David
authors.initials: D
authors.lastname: Thomas
authors.affiliation: Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK.
authors.forename: Chris
authors.initials: C
authors.lastname: Finan
authors.affiliation: Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK.
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Newport
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: Susan
authors.initials: S
authors.lastname: Jones
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D019277:Entropy; D020869:Gene Expression Profiling; D020043:Genes, Essential; D006801:Humans; D009928:Organ Specificity; D011401:Promoter Regions, Genetic
chemical_list: D004247:DNA