Literature DB >> 16241526

Sampling properties of random graphs: the degree distribution.

Michael P H Stumpf1, Carsten Wiuf.   

Abstract

We discuss two sampling schemes for selecting random subnets from a network, random sampling and connectivity dependent sampling, and investigate how the degree distribution of a node in the network is affected by the two types of sampling. Here we derive a necessary and sufficient condition that guarantees that the degree distributions of the subnet and the true network belong to the same family of probability distributions. For completely random sampling of nodes we find that this condition is satisfied by classical random graphs; for the vast majority of networks this condition will, however, not be met. We furthermore discuss the case where the probability of sampling a node depends on the degree of a node and we find that even classical random graphs are no longer closed under this sampling regime. We conclude by relating the results to real Eschericia coli protein interaction network data.

Entities:  

Year:  2005        PMID: 16241526     DOI: 10.1103/PhysRevE.72.036118

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  11 in total

1.  Incomplete and noisy network data as a percolation process.

Authors:  Michael P H Stumpf; Carsten Wiuf
Journal:  J R Soc Interface       Date:  2010-04-08       Impact factor: 4.118

2.  Quantifying noise in mass spectrometry and yeast two-hybrid protein interaction detection experiments.

Authors:  A Annibale; A C C Coolen; N Planell-Morell
Journal:  J R Soc Interface       Date:  2015-09-06       Impact factor: 4.118

Review 3.  Complex networks and simple models in biology.

Authors:  Eric de Silva; Michael P H Stumpf
Journal:  J R Soc Interface       Date:  2005-12-22       Impact factor: 4.118

4.  What you see is not what you get: how sampling affects macroscopic features of biological networks.

Authors:  A Annibale; A C C Coolen
Journal:  Interface Focus       Date:  2011-10-05       Impact factor: 3.906

5.  Estimating the size of the human interactome.

Authors:  Michael P H Stumpf; Thomas Thorne; Eric de Silva; Ronald Stewart; Hyeong Jun An; Michael Lappe; Carsten Wiuf
Journal:  Proc Natl Acad Sci U S A       Date:  2008-05-12       Impact factor: 11.205

6.  Coverage and error models of protein-protein interaction data by directed graph analysis.

Authors:  Tony Chiang; Denise Scholtens; Deepayan Sarkar; Robert Gentleman; Wolfgang Huber
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

7.  The effects of incomplete protein interaction data on structural and evolutionary inferences.

Authors:  Eric de Silva; Thomas Thorne; Piers Ingram; Ino Agrafioti; Jonathan Swire; Carsten Wiuf; Michael P H Stumpf
Journal:  BMC Biol       Date:  2006-11-03       Impact factor: 7.431

8.  Sampling for global epidemic models and the topology of an international airport network.

Authors:  Georgiy Bobashev; Robert J Morris; D Michael Goedecke
Journal:  PLoS One       Date:  2008-09-08       Impact factor: 3.240

Review 9.  Making the most of high-throughput protein-interaction data.

Authors:  Robert Gentleman; Wolfgang Huber
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

10.  Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

Authors:  Ling Yang; Thomas M Vondriska; Zhangang Han; W Robb Maclellan; James N Weiss; Zhilin Qu
Journal:  BMC Bioinformatics       Date:  2008-07-03       Impact factor: 3.169

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