Table 4

Isochores and gene density

Source of gene models

IsoFinder

GC-Profile

BASIO

Least-squares

Average*

Consensus


UCSC known genes

0.696

0.681

0.703

0.693

0.693

0.708


For each isochore map, the gene density (number of genes per Mb) in each of the isochore families L1 to H3 was calculated. Shown is the slope of a linear regression line of the logarithmized densities versus the isochore families. For computing the regression, the isochore families were treated as numbers, from 1 for the L1 family to 5 for the H3 family. Firstly, one can see that gene density is positively correlated with isochore families as all values are positive. Secondly, the consensus isochore map explains gene density best as the slope of the consensus method is greatest. A greater line slope means less gene density in the L isochores and a higher gene density in the H isochores. This is exactly what would be expected in a model with the best fit to the biological hypothesis. *The average gene density of all methods except the consensus isochore map.

Schmidt and Frishman Genome Biology 2008 9:R104   doi:10.1186/gb-2008-9-6-r104

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