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By combining diverse types of annotation, we can better understand the function of a given gene in a breadth of tissues and organ systems and of the biological processes it is involved in the organismal level, as well as its role in disease.
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Both overall levels of replication and breadth of tissue tropism may be positively correlated with virulence.
We describe a computational pipeline that uses microarray data to assess the level of expression and breadth of tissue profiles for transcripts with distinct first exons regulated by alternative promoters.
It is probable then, that there are differences in selection on protein sequences of males and females independent of the breadth of tissue expression.
The breadth of this tissue and species data allows us to show that downregulation of target genes by miRNAs is more pronounced between tissues than between species and that downregulation is more pronounced for genes with fewer binding sites for expressed miRNAs.
To examine the breadth of tissue expression of genes represented by the top 100 ranked clones, we mined the summary SAGE expression data from the Cancer Gene Anatomy Project http://cgap.nci.nih.gov/.
In multicellular organisms the correlation between dN/dS and expression breadth (number of tissues where genes are expressed) is often stronger than with the actual level of gene expression [ 54, 55, 61].
Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.
The microarray expression data described above were used to calculate three measurements of gene expression: peak expression (PE), breadth of expression (BE) and tissue-specificity (TS).
The two factors with the strongest associations with other data types in humans are expression breadth (the number of tissues one protein is expressed in) and phyletic age (defined by the evolutionarily most distant species where homologs can be found) [ 1, 2].
For the analysis of tissue specificity of expression, two separate measures of tissue specificity were used: percentage breadth of expression and PEMMAX.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com