Limits...
Assignment of isochores for all completely sequenced vertebrate genomes using a consensus.

Schmidt T, Frishman D - Genome Biol. (2008)

Bottom Line: We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution.We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, D-85350 Freising, Germany.

ABSTRACT
We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution. We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

Show MeSH

Related in: MedlinePlus

Correlation between isochore classification and gene density. (a) A comparison of the gene density in the consensus isochore map and the GC-Profile segmentation. The underlined data labels denote the gene densities of the GC-Profile segmentation, the non-underlined labels the gene densities of the consensus map. In the consensus assignment more genes can be found in the H3 isochore family than in the GC-Profile assignment. The consensus assignment thus provides a stronger signal in terms of the expected correlation between gene density and isochore class. (b) Linear regression lines of the logarithmized (base 10) gene density values for the isochore families L1 to H3. The isochore families were numbered from 1 to 5 to compute the regression. The slope of the regression line is slightly greater for the consensus isochore map.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2481423&req=5

Figure 4: Correlation between isochore classification and gene density. (a) A comparison of the gene density in the consensus isochore map and the GC-Profile segmentation. The underlined data labels denote the gene densities of the GC-Profile segmentation, the non-underlined labels the gene densities of the consensus map. In the consensus assignment more genes can be found in the H3 isochore family than in the GC-Profile assignment. The consensus assignment thus provides a stronger signal in terms of the expected correlation between gene density and isochore class. (b) Linear regression lines of the logarithmized (base 10) gene density values for the isochore families L1 to H3. The isochore families were numbered from 1 to 5 to compute the regression. The slope of the regression line is slightly greater for the consensus isochore map.

Mentions: We compared the different isochore maps with respect to the degree of correlation between genome segmentation and gene density. As an example, Figure 4a shows a comparison between GC-Profile and the consensus method. Both methods display a clear dependence on the isochore classification of genomic regions, with gene density varying over a broad range between 5 (for both GC-Profile and the consensus map in the L1 isochore) and 73 or 92 (for GC-Profile and the consensus map, respectively, in the H3 isochore). The consensus assignment thus conforms better to the intuitive isochore-gene density model in that it displays higher gene density in the H3 isochore (Figure 4a). Therefore, the consensus isochore assignment provides a stronger signal in terms of gene density-isochore correlation than the GC-Profile segmentation.


Assignment of isochores for all completely sequenced vertebrate genomes using a consensus.

Schmidt T, Frishman D - Genome Biol. (2008)

Correlation between isochore classification and gene density. (a) A comparison of the gene density in the consensus isochore map and the GC-Profile segmentation. The underlined data labels denote the gene densities of the GC-Profile segmentation, the non-underlined labels the gene densities of the consensus map. In the consensus assignment more genes can be found in the H3 isochore family than in the GC-Profile assignment. The consensus assignment thus provides a stronger signal in terms of the expected correlation between gene density and isochore class. (b) Linear regression lines of the logarithmized (base 10) gene density values for the isochore families L1 to H3. The isochore families were numbered from 1 to 5 to compute the regression. The slope of the regression line is slightly greater for the consensus isochore map.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2481423&req=5

Figure 4: Correlation between isochore classification and gene density. (a) A comparison of the gene density in the consensus isochore map and the GC-Profile segmentation. The underlined data labels denote the gene densities of the GC-Profile segmentation, the non-underlined labels the gene densities of the consensus map. In the consensus assignment more genes can be found in the H3 isochore family than in the GC-Profile assignment. The consensus assignment thus provides a stronger signal in terms of the expected correlation between gene density and isochore class. (b) Linear regression lines of the logarithmized (base 10) gene density values for the isochore families L1 to H3. The isochore families were numbered from 1 to 5 to compute the regression. The slope of the regression line is slightly greater for the consensus isochore map.
Mentions: We compared the different isochore maps with respect to the degree of correlation between genome segmentation and gene density. As an example, Figure 4a shows a comparison between GC-Profile and the consensus method. Both methods display a clear dependence on the isochore classification of genomic regions, with gene density varying over a broad range between 5 (for both GC-Profile and the consensus map in the L1 isochore) and 73 or 92 (for GC-Profile and the consensus map, respectively, in the H3 isochore). The consensus assignment thus conforms better to the intuitive isochore-gene density model in that it displays higher gene density in the H3 isochore (Figure 4a). Therefore, the consensus isochore assignment provides a stronger signal in terms of gene density-isochore correlation than the GC-Profile segmentation.

Bottom Line: We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution.We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, D-85350 Freising, Germany.

ABSTRACT
We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution. We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.

Show MeSH
Related in: MedlinePlus