title: Promoter features related to tissue specificity as measured by Shannon entropy.
abstract: BACKGROUND
  The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys provides a means of identifying the general principles for these mechanisms.
  
  
  RESULTS
  We introduce a definition of tissue specificity based on Shannon entropy to rank human genes according to their overall tissue specificity and by their specificity to particular tissues. We apply our definition to microarray-based and expressed sequence tag (EST)-based expression data for human genes and use similar data for mouse genes to validate our results. We show that most genes show statistically significant tissue-dependent variations in expression level. We find that the most tissue-specific genes typically have a TATA box, no CpG island, and often code for extracellular proteins. As expected, CpG islands are found in most of the least tissue-specific genes, which often code for proteins located in the nucleus or mitochondrion. The class of genes with no CpG island or TATA box are the most common mid-specificity genes and commonly code for proteins located in a membrane. Sp1 was found to be a weak indicator of less-specific expression. YY1 binding sites, either as initiators or as downstream sites, were strongly associated with the least-specific genes.
  
  
  CONCLUSIONS
  We have begun to understand the components of promoters that distinguish tissue-specific from ubiquitous genes, to identify associations that can predict the broad class of gene expression from sequence data alone.
authors.affiliation: Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA. jschug@pcbi.upenn.edu
authors.forename: Jonathan
authors.initials: J
authors.lastname: Schug
authors.forename: Winfried-Paul
authors.initials: WP
authors.lastname: Schuller
authors.forename: Claudia
authors.initials: C
authors.lastname: Kappen
authors.forename: J Michael
authors.initials: JM
authors.lastname: Salbaum
authors.forename: Maja
authors.initials: M
authors.lastname: Bucan
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D001665:Binding Sites / Q000235:genetics; D016000:Cluster Analysis; D018899:CpG Islands / Q000235:genetics; D019277:Entropy; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics*; D005796:Genes / Q000235:genetics; D006801:Humans; D051379:Mice; D009928:Organ Specificity; D011401:Promoter Regions, Genetic / Q000235:genetics*; D016329:Sp1 Transcription Factor / Q000378:metabolism; D016385:TATA Box / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D050986:YY1 Transcription Factor / Q000378:metabolism
chemical_list: D016329:Sp1 Transcription Factor; D014157:Transcription Factors; D050986:YY1 Transcription Factor