SigWinR Ridgeogram identifying ROCAGES in Down syndrome data. Ridgeograms of human chromosome 21 from the SigWinR analysis of Down syndrome (trisomy 21) transcriptome data . Left: Input-sequence values are the per gene t-values, i.e fold change of gene-expression log ratios of Down and control samples divided by their standard error. Right: Input-sequence values are the p-values, which indicate the statistical significance of the gene-expression differences between Down and control samples. The data for all chromosomes concatenated has been used as input for the analysis, the result for chromosome 21 was extracted from the genome wide Ridgeogram. Using both types of input-sequence value results in detection of regions of co-altered gene expression (ROCAGEs). As expected, both Ridgeograms show clear ROCAGEs in the analysis of the chromosomal trisomy typifying this syndrome. The Ridgeograms of all chromosomes from these analyses are presented in the Additional files 2 and 3, respectively, the R code and data used to generate the figures can be downloaded from the project home page.