1,768 research outputs found
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks
The idea of 'date' and 'party' hubs has been influential in the study of
protein-protein interaction networks. Date hubs display low co-expression with
their partners, whilst party hubs have high co-expression. It was proposed that
party hubs are local coordinators whereas date hubs are global connectors. Here
we show that the reported importance of date hubs to network connectivity can
in fact be attributed to a tiny subset of them. Crucially, these few, extremely
central, hubs do not display particularly low expression correlation,
undermining the idea of a link between this quantity and hub function. The
date/party distinction was originally motivated by an approximately bimodal
distribution of hub co-expression; we show that this feature is not always
robust to methodological changes. Additionally, topological properties of hubs
do not in general correlate with co-expression. Thus, we suggest that a
date/party dichotomy is not meaningful and it might be more useful to conceive
of roles for protein-protein interactions rather than individual proteins. We
find significant correlations between interaction centrality and the functional
similarity of the interacting proteins.Comment: 27 pages, 5 main figures, 4 supplementary figure
Graph Theory and Networks in Biology
In this paper, we present a survey of the use of graph theoretical techniques
in Biology. In particular, we discuss recent work on identifying and modelling
the structure of bio-molecular networks, as well as the application of
centrality measures to interaction networks and research on the hierarchical
structure of such networks and network motifs. Work on the link between
structural network properties and dynamics is also described, with emphasis on
synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape
The Dichotomy in Degree Correlation of Biological Networks
Most complex networks from different areas such as biology, sociology or technology, show a correlation on node degree where the possibility of a link between two nodes depends on their connectivity. It is widely believed that complex networks are either disassortative (links between hubs are systematically suppressed) or assortative (links between hubs are enhanced). In this paper, we analyze a variety of biological networks and find that they generally show a dichotomous degree correlation. We find that many properties of biological networks can be explained by this dichotomy in degree correlation, including the neighborhood connectivity, the sickle-shaped clustering coefficient distribution and the modularity structure. This dichotomy distinguishes biological networks from real disassortative networks or assortative networks such as the Internet and social networks. We suggest that the modular structure of networks accounts for the dichotomy in degree correlation and vice versa, shedding light on the source of modularity in biological networks. We further show that a robust and well connected network necessitates the dichotomy of degree correlation, suggestive of an evolutionary motivation for its existence. Finally, we suggest that a dichotomous degree correlation favors a centrally connected modular network, by which the integrity of network and specificity of modules might be reconciled
Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity
The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification
<p>Abstract</p> <p>Background</p> <p>A molecular network perspective forms the foundation of systems biology. A common practice in analyzing protein-protein interaction (PPI) networks is to perform network analysis on a conglomerate network that is an assembly of all available binary interactions in a given organism from diverse data sources. Recent studies on network dynamics suggested that this approach might have ignored the dynamic nature of context-dependent molecular systems.</p> <p>Results</p> <p>In this study, we employed a network stratification strategy to investigate the validity of the current network analysis on conglomerate PPI networks. Using the genome-scale tissue- and condition-specific proteomics data in <it>Arabidopsis thaliana</it>, we present here the first systematic investigation into this question. We stratified a conglomerate <it>A. thaliana </it>PPI network into three levels of context-dependent subnetworks. We then focused on three types of most commonly conducted network analyses, i.e., topological, functional and modular analyses, and compared the results from these network analyses on the conglomerate network and five stratified context-dependent subnetworks corresponding to specific tissues.</p> <p>Conclusions</p> <p>We found that the results based on the conglomerate PPI network are often significantly different from those of context-dependent subnetworks corresponding to specific tissues or conditions. This conclusion depends neither on relatively arbitrary cutoffs (such as those defining network hubs or bottlenecks), nor on specific network clustering algorithms for module extraction, nor on the possible high false positive rates of binary interactions in PPI networks. We also found that our conclusions are likely to be valid in human PPI networks. Furthermore, network stratification may help resolve many controversies in current research of systems biology.</p
Network analyses in systems biology: new strategies for dealing with biological complexity
The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity
Communities in C.elegans connectome through the prism of non-backtracking walks
The fundamental relationship between the mesoscopic structure of neuronal
circuits and organismic functions they subserve is one of the major challenges
in contemporary neuroscience. Formation of structurally connected modules of
neurons enacts the conversion from single-cell firing to large-scale behaviour
of an organism, highlighting the importance of their accurate profiling in the
data. While connectomes are typically characterized by significant sparsity of
neuronal connections, recent advances in network theory and machine learning
have revealed fundamental limitations of traditionally used community detection
approaches in cases where the network is sparse. Here we studied the optimal
community structure in the structural connectome of C.elegans, for which we
exploited a non-conventional approach that is based on non-backtracking random
walks, virtually eliminating the sparsity issue. In full agreement with the
previous asymptotic results, we demonstrated that non-backtracking walks
resolve the ground truth annotation into clusters on stochastic block models
(SBM) with the size and density of the connectome better than the spectral
methods related to simple random walks. Based on the cluster detectability
threshold, we determined that the optimal number of modules in a recently
mapped connectome of C.elegans is 10, which precisely corresponds to the number
of isolated eigenvalues in the spectrum of the non-backtracking flow matrix.
Broadly, our work provides a robust network-based framework to reveal
mesoscopic structures in sparse connectomic datasets, paving way to further
investigation of connectome mechanisms for different functions.Comment: This work previously appeared as arXiv:2207.00767 under an accidental
replacemen
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