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Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs representing metabolic and protein-protein interaction (PPI) networks. First, we investigate the quality of fits obtained for the nodes degree distributions to power-law functions. This analysis suggests that a power-law distribution poorly describes the data except for the far right tail in the case of PPI networks. Next we obtain descriptive statistics for the main graph parameters and try to identify the properties that deviate from the expected values had the networks been built by randomly linking nodes with the same degree distribution. This survey identifies the properties of biological networks which are not solely the result of their degree distribution, but emerge from yet unidentified mechanisms other than those that drive these distributions. The findings suggest that, while PPI networks have properties that differ from their expected values in their randomiz
Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and glo
The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death. Here we char
From the spectral plot of the (normalized) graph Laplacian, the essential qualitative properties of a network can be simultaneously deduced. Given a class of empirical networks, reconstruction schemes for elucidating the evolutionary dynamics leading
The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional form contai