Databases and Systems

Figure 3: Universal Coordinate Dispersion Plot of Chromosome 3
How important is this dispersion? Is it worth worrying about? When universal
coordinates are used to support queries of the content of a region, dispersion can
cause both false negative and false positive errors in the results, i.e., they can fail to
retrieve the appropriate parts of some maps and retrieve inappropriate parts of others
(see Figure 4). In figure 3 the dispersion appears to be on the order of about 5% of
the chromosome length; intuitively that means that at resolutions finer than this the
alignments are not reliable.
Figure 4: Query region does not find completely corresponding regions of maps due
to nonlinear alignment
One surprising aspect of dispersion is that there is no dispersion associated with
points that occur on only one map, because a single regression line transforms them
to a unique universal coordinate. It happens that cytogenetic band boundaries occur
only on the cytogenetic maps, so they get assigned a single unique coordinate, as if
they were very precisely localized. A marker which has been used as a landmark on
many maps will by contrast be associated with a cloud of points in universal
coordinates, suggesting that it has a fuzzy localization, whereas in fact we have much
more information about its position than we do about something like a band
boundary. When cytogenetic bands are used to define the region of interest for a
positional query, this spurious accuracy in their universal coordinates can give
anomalous results: regions of non-cytogenetic maps which are known to be located in
a given band on the cytogenetic map may not be retrieved by a universal coordinate
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