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Entropy synonym3/16/2023 ![]() ![]() It is desirable to re-examine this finding in the context of complete genomes for human and mouse and to place it in context with subsequent findings such as the association of CpG islands with embryonic expression. For example, based on the limited number of genes available at the time of the analysis, promoters with CpG islands have been associated with housekeeping genes. While the details of regulatory mechanisms will vary for individual genes, general features of promoters (and here we will restrict our focus to RNA polymerase II (Pol II) promoters) are likely to facilitate whether a gene will be expressed widely or in a restricted manner. Both types of genes may be needed for embryonic development as well as for the function of adult cells and tissues. Basic cellular functions require the expression of certain genes in all cells and tissues (that is, in a ubiquitous manner) while specialized functions require restricted expression of other genes in a single or small number of cells and tissues (that is, tissue specific). The development of an adult from the single cell of a fertilized egg requires a complex orchestration of genes to be expressed at the right time, place, and level. 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. YY1 binding sites, either as initiators or as downstream sites, were strongly associated with the least-specific genes. Sp1 was found to be a weak indicator of less-specific expression. 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. 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. We find that the most tissue-specific genes typically have a TATA box, no CpG island, and often code for extracellular proteins. We show that most genes show statistically significant tissue-dependent variations in expression level. ![]() 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 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. ![]() 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. The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. ![]()
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