Skew profiles

B. Transcription-Induced Step-like Skew Profiles in the Human Genome... 

From the skews 5 ta( ). 5gc( ). and S n), obtained along the sequences, where n is the position (in kbp units) from the origin, we also computed the cumulative skew profiles ... 

Figure 10. Cumulated skew profiles calculated around the origin of replication DNMTl Lamin B2, and P-globin in the human genome Sm (thick line) and Sec (thin line). The colors have the same meaning as in Fig. 9. See color insert.

In Fig. 17 is shown the mean skew profile calculated in intergenic windows on both sides of the 1012 putative replication origins [38]. This mean skew profile presents a rather sharp transition from negative to positive values when crossing the origin position. To avoid any bias in the skew values that could... 

Figure 17. Mean skew profile of intergenic regions around putative replication origins [38]. The skew S was calculated in 1 kbp windows (Watson strand) around the position ( 300 kbp without repeats) of the 1012 detected upward jumps 5 and 3 transcript extremities were extended by 0.5 and 2 kbp, respectively ( ), or by 10 kbp at both ends ( ). The abscissa represents the distance (in kbp) to the corresponding origin the ordinate represents the skews calculated for the windows situated in intergenic regions (mean values for all discontinuities and for 10 consecutive 1-kbp window positions). The skews are given in percent (vertical bars, SEM). The lines correspond to linear fits of the values of the skew ( ) for n < —100 kbp and n > 100 kbp.

Figure 14. (a) Skew profiles of a fragment of human chromosome 12. (b) WT of S using... 

Wj(i) [S](n, d) is coded from black (min) to red (max) three cuts of the WT at constant scale a = a = 200 kbp, 70 kbp and 20 kbp are superimposed together with five maxima lines identified as pointing to upward jumps in the skew profile, (c) WT skeleton defined by the maxima lines in blue (respectively, red) when corresponding to positive (respectively, negative) values of the WT. At the scale a = 200 kbp, one thus identify 7 upward (blue dots) and 8 downward (red dots) jumps. The black dots in (b) correspond to the five WTMM of largest amplitude that have been identified as putative replication origins it is clear that the associated maxima hues point to the five major upward jumps in the skew profile in the limit a — 0+. 

Fig. 8.2. Compared with the narrow peak in the normal histogram at the upper left, it can be seen that a single peak with a wide coefficient of variation (CV) or skewed profile may mask a near-diploid malignant cell line. In addition, an extra small peak at the 4C position may result from clumping of nuclei, cycling cells, or a true tetra-ploid abnormality. Data courtesy of Colm Hennessy.

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