Impact of observational incompleteness on the structural properties of protein interaction networks
Last modified: April 21, 2006
The observed structure of protein interaction networks is corrupted by
many false positive/negative links. This observational incompleteness
is abstracted as random link removal and a specific, experimentally
motivated (spoke) link rearrangement. Their impact on the structural
properties of gene-duplication-and-mutation network models is studied.
For the degree distribution a curve collapse is found, showing no
sensitive dependence on the link removal/rearrangement strengths and
disallowing a quantitative extraction of model parameters. The spoke
link rearrangement process moves other structural observables,
like degree correlations, cluster coefficient and motif frequencies,
closer to their counterparts extracted from the yeast data. This
underlines the importance to take a precise modeling of the
observational incompleteness into account when network structure
models are to be quantitatively compared to data.