ArticleBMC biology2006
The effects of incomplete protein interaction data on structural and evolutionary inferences.
Article in BMC biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 67 citations in OpenAlex.
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- Advancing edge-based clustering and graph embedding for biological network analysis: a case study in RASopathies.Briefings in bioinformatics · 2025Article
- Gaining confidence in inferred networks.Scientific reports · 2022Article
- HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks.Nucleic acids research · 2017Article
- Quantifying noise in mass spectrometry and yeast two-hybrid protein interaction detection experiments.Journal of the Royal Society, Interface · 2015Article
- A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize.Frontiers in genetics · 2015Article
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- Analysis of genetic interaction networks shows that alternatively spliced genes are highly versatile.PloS one · 2013Article
- Biological function through network topology: a survey of the human diseasome.Briefings in functional genomics · 2012Article
- Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.BMC systems biology · 2012Article
- Graph spectral analysis of protein interaction network evolution.Journal of the Royal Society, Interface · 2012Article
- Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast.BMC systems biology · 2012Article
- Topological effects of data incompleteness of gene regulatory networks.BMC systems biology · 2012Article
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- What you see is not what you get: how sampling affects macroscopic features of biological networks.Interface focus · 2011Article
- The effects of network neighbours on protein evolution.PloS one · 2011Article
- Incomplete and noisy network data as a percolation process.Journal of the Royal Society, Interface · 2010Article
- Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins.BMC bioinformatics · 2010Article
- Topological network alignment uncovers biological function and phylogeny.Journal of the Royal Society, Interface · 2010Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundPresent protein interaction network data sets include only interactions among subsets of the proteins in an organism. Previously this has been ignored, but in principle any global network analysis that only looks at partial data may be biased. Here we demonstrate the need to consider network sampling properties explicitly and from the outset in any analysis.
resultsHere we study how properties of the yeast protein interaction network are affected by random and non-random sampling schemes using a range of different network statistics. Effects are shown to be independent of the inherent noise in protein interaction data. The effects of the incomplete nature of network data become very noticeable, especially for so-called network motifs. We also consider the effect of incomplete network data on functional and evolutionary inferences.
conclusionCrucially, when only small, partial network data sets are considered, bias is virtually inevitable. Given the scope of effects considered here, previous analyses may have to be carefully reassessed: ignoring the fact that present network data are incomplete will severely affect our ability to understand biological systems.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.