82 CATALYZING INQUIRY
Biologists use a variety of different data representations to help describe, examine, and understand
data. Biologists often use cartoons as conceptual, descriptive models of biological events or processes. A
cartoon might show a time line of events: for example, the time line of the phosphorylation of a receptor
that allows a protein to bind to it. As biologists take into account the simultaneous interactions of larger
numbers of molecules, events over time become more difficult to represent in cartoons. New ways to
“see” interactions and associations are therefore needed in life sciences research.
The most complex data visualizations are likely to be representations of networks. The complete
graph in Figure 4.2 contains 4,543 nodes of approximately 6,000 proteins encoded by the yeast genome,
along with 12,843 interactions. The graph was developed using the Osprey network visualization system.
FIGURE 4.2 From genomics to proteomics. Visualization of combined, large-scale interaction data sets in yeast. A
total of 14,000 physical interactions obtained from the GRID database were represented with the Osprey network
visualization system (see http://biodata.mshri.on.ca/grid)..) Each edge in the graph represents an interaction be-
tween nodes, which are colored according to Gene Ontology (GO) functional annotation. Highly connected com-
plexes within the dataset, shown at the perimeter of the central mass, are built from nodes that share at least three
interactions within other complex members. The complete graph contains 4,543 nodes of ~6,000 proteins encoded
by the yeast genome, 12,843 interactions and an average connectivity of 2.82 per node. The 20 highly connected
complexes contain 340 genes, 1,835 connections, and an average connectivity of 5.39.
SOURCE: Reprinted by permission from M. Tyers and M. Mann, “From Genomics to Proteomics,” Nature 422:193-
197, 2003. Copyright 2003 Macmillan Magazines Ltd.