ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality

Szalay-Bekő, Máté; Palotai, Robin; Szappanos, Balázs; Kovács, I.; Papp, Balázs; Csermely, Péter

doi:10.1093/bioinformatics/bts352

Cited by 98 publications

(134 citation statements)

References 45 publications

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“…To identify important hubs in the network, centrality was assessed. "Betweenness centrality" measures how often a path passes through a specific node while moving from one node to another (22).…”

Section: Methodsmentioning

confidence: 99%

Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives

Rokop

Horton

Newton

2015

Appl Environ Microbiol

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In contrast to the honey bee gut, which is colonized by a few characteristic bacterial clades, the hive of the honey bee is home to a diverse array of microbes, including many lactic acid bacteria (LAB). In this study, we used culture, combined with sequencing, to sample the LAB communities found across hive environments. Specifically, we sought to use network analysis to identify microbial hubs sharing nearly identical operational taxonomic units, evidence which may indicate cooccurrence of bacteria between environments. In the process, we identified interactions between noncore bacterial members (Fructobacillus and Lactobacillaceae) and honey bee-specific "core" members. Both Fructobacillus and Lactobacillaceae colonize brood cells, bee bread, and nectar and may serve the role of pioneering species, establishing an environment conducive to the inoculation by honey bee core bacteria. Coculture assays showed that these noncore bacterial members promote the growth of honey bee-specific bacterial species. Specifically, Fructobacillus by-products in spent medium supported the growth of the Firm-5 honey bee-specific clade in vitro. Metabolic characterization of Fructobacillus using carbohydrate utilization assays revealed that this strain is capable of utilizing the simple sugars fructose and glucose, as well as the complex plant carbohydrate lignin. We tested Fructobacillus for antibiotic sensitivity and found that this bacterium, which may be important for establishment of the microbiome, is sensitive to the commonly used antibiotic tetracycline. Our results point to the possible significance of "noncore" and environmental microbial community members in the modulation of honey bee microbiome dynamics and suggest that tetracycline use by beekeepers should be limited.

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Section: Methodsmentioning

confidence: 99%

Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives

Rokop

Horton

Newton

2015

Appl Environ Microbiol

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“…It has been shown that many proteins have a modular architecture, with modules corresponding to (often functionally distinct) subdomains. Residues between modules tend to be conserved and more rigid, and are thought to be involved in allosteric communication [66][67][68][69]. Several studies have employed the concept of modules or a related notion [69][70][71].…”

Section: Methods To Identify Allosteric Pathways In Intraprotein Netwmentioning

confidence: 99%

“…We may use a number of centrality measures [194], including perturbation-based or game-theoretical assumptions [115,195], to find the level of importance of proteins and pathways in interactomes and signaling networks, and important amino acids in their extensions to atomic level resolution [69].…”

Section: Possible Methods To Identify Allo-network Drug Targetsmentioning

confidence: 99%

Allo-Network Drugs: Extension of the Allosteric Drug Concept to Protein- Protein Interaction and Signaling Networks

Szilágyi¹,

Nussinov²,

Csermely

2013

CTMC

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Allosteric drugs are usually more specific and have fewer side effects than orthosteric drugs targeting the same protein. Here, we overview the current knowledge on allosteric signal transmission from the network point of view, and show that most intra-protein conformational changes may be dynamically transmitted across protein-protein interaction and signaling networks of the cell. Allo-network drugs influence the pharmacological target protein indirectly using specific inter-protein network pathways. We show that allo-network drugs may have a higher efficiency to change the networks of human cells than those of other organisms, and can be designed to have specific effects on cells in a diseased state. Finally, we summarize possible methods to identify allo-network drug targets and sites, which may develop to a promising new area of systems-based drug design.

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“…Extending these observations further in a former study [54] we used the ModuLand program package [76] and its Cytoscape plug-in [93] to identify extensively overlapping network modules of the protein-protein interaction network of S. cerevisiae under fast-growing conditions and after various stresses. Upon a 15 minute, heat shock at 37°C, the overlap between yeast interactome modules became significantly smaller.…”

Section: Short-term Adaptive Changes Of Cellular Network: Changes Ofmentioning

confidence: 99%

System Level Mechanisms of Adaptation, Learning, Memory Formation and Evolvability: The Role of Chaperone and Other Networks

Gyurko

Sőti

Steták

et al. 2014

CPPS

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During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here, we describe first the protein structure networks of molecular chaperones, then characterize chaperone containing sub-networks of interactomes called as chaperone-networks or chaperomes. We review the role of molecular chaperones in short-term adaptation of cellular networks in response to stress, and in long-term adaptation discussing their putative functions in the regulation of evolvability. We provide a general overview of possible network mechanisms of adaptation, learning and memory formation. We propose that changes of network rigidity play a key role in learning and memory formation processes. Flexible network topology provides 'learningcompetent' state. Here, networks may have much less modular boundaries than locally rigid, highly modular networks, where the learnt information has already been consolidated in a memory formation process. Since modular boundaries are efficient filters of information, in the 'learning-competent' state information filtering may be much smaller, than after memory formation. This mechanism restricts high information transfer to the 'learning competent' state. After memory formation, modular boundary-induced segregation and information filtering protect the stored information. The flexible networks of young organisms are generally in a 'learning competent' state. On the contrary, locally rigid networks of old organisms have lost their 'learning competent' state, but store and protect their learnt information efficiently. We anticipate that the above mechanism may operate at the level of both protein-protein interaction and neuronal networks.

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ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality

Abstract: The plug-in and its user guide can be downloaded freely from: http://www.linkgroup.hu/modules.php.

Cited by 98 publications

References 45 publications

Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives

Interactions between Cooccurring Lactic Acid Bacteria in Honey Bee Hives

Allo-Network Drugs: Extension of the Allosteric Drug Concept to Protein- Protein Interaction and Signaling Networks

System Level Mechanisms of Adaptation, Learning, Memory Formation and Evolvability: The Role of Chaperone and Other Networks

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