Figure 1

Using a mmFDR method to detect RIDGEs in a human transcriptome map. Schematic representation of the moving median false discovery rate (mmFDR) procedure identifying regions of high and low density of gene expression (RIDGEs and anti-RIDGEs, respectively) [4]. (A) Input sequence, a human transcriptome map (HTM), i.e., expression values of genes ordered by their chromosome location (cyan; chromosome 6). (B) mm(w), moving medians of the HTM for a given window size S. (C) Determination of the high and low mmFDR thresholds at a given level α: The high threshold m _k is the smallest gene expression value for which the ${\displaystyle {\sum }_{m\ge m_k}f(m)/{\displaystyle {\sum }_{m\ge m_k}g(m)\le \alpha }}$, here f(m) is the theoretical probability distribution of mm(w), and g(m) is the observed distribution of mm(w). (In [4], f(m) is estimated by simple sampling). Similarly, the low threshold m _j is the largest gene expression value for which ${\displaystyle {\sum }_{m\le m_j}f(m)/{\displaystyle {\sum }_{m\le m_j}g(m)\le \alpha }}$. (D) Selection of significant windows in chromosome 6: RIDGEs (in red) all windows for which the median gene expression is higher than or equal to m _k ; anti-RIDGEs (in blue) all windows for which the median gene expression is lower than or equal to m _j . (E) Output RIDGEOGRAM of chromosome 6. Each row (y-axis) in the RIDGEOGRAM represents a window size, ranging from S = 3 to S = M (the number of genes on the chromosome). Each column (x-axis) represents a sliding window number, ranging from w = S/2 to w = M-S/2 (hence the triangular form). Color is used to mark window medians significantly above (red) or below (blue) the genome-wide median. The scheme shows median expression data for window size S = 69 and FDR thresholds level α = 5%.