Isochore assignment confidence in border regions. (a) On average the isochore assignment confidence is lowest near borders. Here the borders of all isochore maps were used. Assignment confidence grows with the distance from the border and reaches saturation at a distance of about 0.2 Mb from the border. This can be considered as an empirically derived 'safe distance' threshold. (b) Variance of the assignment confidence is almost independent of the border distance.

GC differences between neighboring isochores. The distribution of GC differences between adjacent isochores is shown for each method. The thick bars within each box plot indicate the median. The IsoFinder and GC-Profile assignments have the largest GC deltas, on average, whereas in the BASIO isochore map the GC deltas are lowest (median 3.5, mean 4.0). Outliers are not shown in this plot. The average delta GC in the consensus map is 4.6, the median 4.1.

Isochore assignment confidence and GC context. (a) Confidence as a function of the GC content of the genomic environment. Isochore assignment confidence is best in GC-poor regions; it decreases as the genomic context becomes more GC-rich and reaches a minimum around 55-58% GC. However, the assignment confidence becomes better again in the GC-richest regions with >59% GC. (b) Variance of the confidence depending on the GC content. The confidence variance is independent of the GC context for isochores with a GC content between about 33% and 62% GC, that is, for the main bulk of the genomic DNA.

Comparison of isochore assignments in the human genome made by the different methods. All isochore maps show remarkable differences with respect to the number and the average length of their isochore segments. The IsoFinder and BASIO methods result in the most fine-grained segmentations while GC-Profile and least-squares produce less fragmented partitioning of the genome. The consensus map provides a compromise solution. (a) Number of isochore stretches. (b) Average isochore length.

Graphical representation of the isochore assignments for the first 100 Mb of the human chromosome 1 (obtained from the IsoBase web page [25]). (a) Consensus assignment. The color code depicts the isochore families as defined by Bernardi et al. [26,18](b) Confidence of the assignments. For each residue the number of isochore methods that support a given isochore class is depicted as a red line. Support values for individual bases are averaged over a sliding window (blue line). (c) Isochore predictions made by each of the available methods.

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.

Isochore assignment confidence of human genes. Each bin of the histogram shows the percentage of genes supported by a given average number of computational methods. Denoted is the upper border of each bin. Each bin shows the number of genes having an isochore assignment confidence c with lower-border < c ≤ upper border. For example, 30% of genes have a confidence value of >1.8 and ≤ 2.0. About one-third (29%, the right-most bar) of all genes are equally classified by all four independent methods (BASIO, IsoFinder, GC-Profile and least-squares). Gene classifications with low confidence can hardly be found. For 99.8% of all genes at least two methods agree completely over the whole coding region. Furthermore, only very few genes have a confidence value between two full numbers. This can be explained by two observations: the genes are usually completely located within a single isochore stretch; and these gene regions are hardly separated by any of the segmentation methods. Therefore, usually two, three or all four methods agree for the complete gene. The mean and median support for all genes is 3.0.