Basic networks: Definition and applications

Abstract

We define basic networks as the undirected subgraphs with minimal number of units in which the distances (geodesics, minimal path lengths) among a set of selected nodes, which we call seeds, in the original graph are conserved. The additional nodes required to draw the basic network are called connectors. We describe a heuristic strategy to find the basic networks of complex graphs. We also show how the characterization of these networks may help to obtain relevant biological information from highly complex protein-protein interaction data.

Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell

“…Discussions currently center in the best way to define modules so they make sense from either the mathematical or the biological point of view (e. g. refs. [ 18 - 20 ]), but it is generally accepted that modules are often enriched for particular GO terms. This congruence between GO and PPI data has led to works in which proteins are assigned functions according to the GO annotations of their interaction partners [ 21 - 23 ].…”