A significant challenge to understanding complex datasets such as microarrays and protein-protein interactions is our ability to see the data. Traditional two-dimensional paper presentations are becoming too limited. The size and complexity of data have increased substantially with genomic and proteomic methods.
Many investigators are collaborating with computer scientists and mathematicians to develop new tools to display data in new and dynamic ways. You can explore some efforts being made at these web sites:
1) Cytoscape - protein-protein interactions.
2) H3 Viewer - complex graphs of any type
3) GeneCensus - whole genome information databases (emphasizes mining data rather than visualizing)
4) GenMAPP - Flash animation to demonstrate intersection of microarray data and functional roles of proteins.
5) BIND - java aplet to show protein-protein interactions and protein complexes
6) Cellzome - Yeast (Saccharomyces cerevisiae) protein complex database. Systematic analysis of multiprotein complexes in Saccharomyces cerevisiae, as a model system relevant to human. (free registration to academic users)
7) FlyNets - Drosophila melanogaster molecular interactions and genetic networks.
8) Interact - An Object Oriented Database for Protein-Protein Interactions. To view the 3D world, you must obtain a VRML plugin : cosmoplayer.
9) PIM Rider - Hybrigenics' new functional proteomics software platform, dedicated to the exploration of protein pathways. (Registration required to use, free tour available).
New methods of integrating and visualizing data need to be developed. Keep looking for new methods and see what you can learn when data are displayed in meaningful ways.