Approach to data analysis. A developmental timeline (DT), which is a linear number ray on which each of 5,166 genes has a definite position, is constructed from a time course of gene expression during development (top left panel), positioning genes that are expressed in early development on the left end, genes that are upregulated in late development on the right end and neutral genes in the middle. The DT is integrated with genes that are deregulated in a population of tumors versus corresponding normal tissues (top right panel). (a) Frequency plot showing a histogram-like representation of the frequency of upregulated (red) and downregulated (green) cancer genes in different portions of the DT. The height of each bar indicates how many deregulated genes map to one of 13 equally sized segments of the DT. Each segment corresponds to approximately 400 genes. Up- and downregulated genes are depicted on separate DTs, that is, the first red bar refers to the same DT segment as the first green bar. Stated differently, the height of the first red bar signifies the number of upregulated cancer genes that map to the first 400 developmental genes and the height of the first green bar signifies the number of downregulated cancer genes that map to the same set of 400 developmental genes. (b) Probability density plot showing P(DEV[1,2,3...i] | cancer) for i = 2,3...5,166 for upregulated and downregulated cancer genes. The probability of being among the first i genes on the DT (genes are numbered 1-5,166 from left/early to right/late) if deregulated in cancer directly reflects the preference of cancer genes for different segments of the DT. The shape of each probability distribution is summarized by two linear functions that are fitted to its early and late portions (blue lines). The slopes of these functions are subsequently used as a quantification of the developmental profile of a cancer.