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Figure 1 | BMC Research Notes

Figure 1

From: SigWinR; the SigWin-detector updated and ported to R

Figure 1

Advanced SigWinR Ridgeogram for RIDGES in the human transcriptome map. An example of SigWinR Ridgeograms (left) and Ridgeplots for pre-defined window sizes (right) for chromosome 1 from the analysis of (anti-)RIDGEs in the human transcriptome map (HTM) [2]. The p-values of the RIDGEs (red) and anti-RIDGES (blue) in the Ridgeograms are indicated by the shade of the colour as shown on the scale bars to the right of the Ridgeograms. Below the Ridgeograms, an XY-plot of the gene-expression values of the whole genome sequence is depicted. In the Ridgeplots the stretches with p-values (corrected for multiple testing) below 0.01 are shown: RIDGES with a red shade, anti-RIDGES with a blue shade. The window size taken to generate the Ridgeplots is indicated by a horizontal bar in the Ridgeograms. The XY-plots beneath the Ridgeogram are shown in non-log space, whereas in the Ridgeplots log values are used. Since the Sigwin algorithm is based on a rank statistics, this is of no influence to the result. Upper part: The input sequence is the genes ordered by their occurrence on the chromosomes. The value of the sequence elements is gene-expression from a serial analysis of gene expression (SAGE) compendium. Lower part: An example of a SigWinR PosRidgeogram for essentially the same analysis, but with an input sequence consisting of 1 kb chromosomal stretches. As such, although the moving window analyses for every line in the Ridgeogram the same chromosomal size, it will contain a variable number of genes. In the Ridgeplot the centromere is clearly visible as a region with a low sample density. The Ridgeograms of all chromosomes from these analyses are presented in the Additional files 1 and 4, respectively.

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