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Promoter features related to tissue specificity as measured by Shannon entropy

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 principle...

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Autores principales: Schug, Jonathan, Schuller, Winfried-Paul, Kappen, Claudia, Salbaum, J Michael, Bucan, Maja, Stoeckert, Christian J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088961/
https://www.ncbi.nlm.nih.gov/pubmed/15833120
http://dx.doi.org/10.1186/gb-2005-6-4-r33
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author Schug, Jonathan
Schuller, Winfried-Paul
Kappen, Claudia
Salbaum, J Michael
Bucan, Maja
Stoeckert, Christian J
author_facet Schug, Jonathan
Schuller, Winfried-Paul
Kappen, Claudia
Salbaum, J Michael
Bucan, Maja
Stoeckert, Christian J
author_sort Schug, Jonathan
collection PubMed
description 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.
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spelling pubmed-10889612005-05-05 Promoter features related to tissue specificity as measured by Shannon entropy Schug, Jonathan Schuller, Winfried-Paul Kappen, Claudia Salbaum, J Michael Bucan, Maja Stoeckert, Christian J Genome Biol Research 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. BioMed Central 2005 2005-03-29 /pmc/articles/PMC1088961/ /pubmed/15833120 http://dx.doi.org/10.1186/gb-2005-6-4-r33 Text en Copyright © 2005 Schug et al.; licensee BioMed Central Ltd.
spellingShingle Research
Schug, Jonathan
Schuller, Winfried-Paul
Kappen, Claudia
Salbaum, J Michael
Bucan, Maja
Stoeckert, Christian J
Promoter features related to tissue specificity as measured by Shannon entropy
title Promoter features related to tissue specificity as measured by Shannon entropy
title_full Promoter features related to tissue specificity as measured by Shannon entropy
title_fullStr Promoter features related to tissue specificity as measured by Shannon entropy
title_full_unstemmed Promoter features related to tissue specificity as measured by Shannon entropy
title_short Promoter features related to tissue specificity as measured by Shannon entropy
title_sort promoter features related to tissue specificity as measured by shannon entropy
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088961/
https://www.ncbi.nlm.nih.gov/pubmed/15833120
http://dx.doi.org/10.1186/gb-2005-6-4-r33
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