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## Figure 1.
Flow diagram of the mathematics of genomic tracks. Genomic tracks are represented as geometric objects on the line defined by the base
pairs of the genome sequence: (unmarked (UP) or marked (MP)) points, (unmarked (US)
or marked (MS)) segments, and functions (F). The biologist identifies the two tracks
to be compared, and the Genomic HyperBrowser detects their type. The biological question
of interest is stated in terms of mathematical relations between the types of the
two tracks. The relevant questions are proposed by the system. The biologist then
selects the question and needs to specify the null hypothesis. For this purpose she
is called to decide about what structures are preserved in each track, and how to
randomize the rest. Thereafter, the Genomic HyperBrowser identifies the relevant test
statistics, and computes actual P-values, either exactly or by Monte Carlo testing. Results are then reported, both
for a global analysis, answering the question on the whole genome (or area of study),
and for a local analysis. Here, the area is divided into bins, and the answer is given
per bin. P-values, test-statistic, and effect sizes are reported, as tables and graphics. Significance
is reported when found, after correction for multiple testing.
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