Topological nature of metabolic networks metabolic networks and pathways. Medical search. Frequent questions

In contrast, in signed networks the similarity between genes reflects the sign of the correlation of their expression profiles. (wikipedia.org)
In this study, we performed a systematic analysis on a set of nicotine addiction-related genes to explore their characteristics at network levels. (hindawi.com)
We found that NAGenes tended to have a more moderate degree and weaker clustering coefficient and to be less central in the network compared to alcohol addiction-related genes or cancer genes. (hindawi.com)
Further, clustering of these genes resulted in six clusters with themes in synaptic transmission, signal transduction, metabolic process, and apoptosis, which provided an intuitional view on the major molecular functions of the genes. (hindawi.com)
Further, emerging evidence suggests that nicotine can also regulate the expression of genes/proteins involved in various functions such as ERK1/2, CREB, and c-FOS [ 20 - 22 ], as well as the expression state of multiple biochemical pathways, for example, mitogen-activated protein kinase (MAPK), phosphatidylinositol phosphatase signaling, growth factor signaling, and ubiquitin-proteasome pathways [ 23 - 25 ]. (hindawi.com)
The immune-related DEOSGs and hub genes were identified by weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) analysis, respectively. (nature.com)
Finally, we constructed the drug, transcription factors (TFs), and microRNA network of the diagnostic genes. (nature.com)
Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
Another cluster included genes encoding enzymes in the mitochondrial beta-oxidation pathway. (biomedcentral.com)
Genes and pathways associated with lactation number in cows were identified for the first time to date, and we found that many were comparable to those known to be associated with ageing in humans and model organisms. (biomedcentral.com)
In this paper, we present CASNet, which aims to identify better ASNs using (i) integrated interaction networks (mixed graphs), (ii) directions of regulations of genes, and (iii) combined node and edge scores. (biomedcentral.com)
Our analysis of a breast cancer dataset finds that the positive feedback loops across 7 genes, AR , ESR 1, MYC , E 2 F 2, PGR , BCL 2 and CCND 1 are conserved across the basal/triple negative subtypes in multiple datasets that could potentially explain the aggressive nature of this cancer subtype. (biomedcentral.com)
Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. (mdpi.com)
The objective of this work is to identify dysregulated genes and pathways of ccRCC temporally according to systematic tracking of the dysregulated modules of reweighted Protein-Protein Interaction (PPI) networks. (hindawi.com)
Finally, gene compositions of altered modules were analyzed, and pathways enrichment analyses of genes in altered modules were carried out based on Expression Analysis Systematic Explored (EASE) test. (hindawi.com)
We successfully identified dysregulated genes and pathways of ccRCC in different stages, and these might be potential biological markers and processes for treatment and etiology mechanism in ccRCC. (hindawi.com)
In addition, a PPI network can be modeled as an undirected graph, where vertices represent proteins and edges represent interactions between proteins, to prioritize disease associated genes or pathways and to understand the modus operandi of disease mechanisms [ 9 , 10 ]. (hindawi.com)
for example, Chu and Chen [ 13 ] combined PPI and gene expression data to construct a cancer perturbed PPI network in cervical carcinoma to study gain- and loss-of-function genes as potential drug targets. (hindawi.com)
14 ] combined PPI and gene expression data to construct tissue-specific PPI networks for 60 tissues and used them to prioritize disease genes. (hindawi.com)
For example, butanol pathway genes from Clostridia were introduced into E. While the introduction of heterologous genes is well established, a major energy-dense liquid biofuel. (margottriesthegoodlife.com)
Network properties of complex human disease genes identified through genome-wide association studies. (leibniz-fli.de)
Next, hypoxia- and immune-related genes were screened by the LASSO + support vector machine recursive feature elimination (SVM-RFE) and weighted gene co-expression network analysis (WGCNA). (biomedcentral.com)
Finally, we constructed a competing endogenous RNA (ceRNA) network of key genes. (biomedcentral.com)

By following a systematic workflow we reconstruct a genome-scale metabolic model for M. acetivorans . (biomedcentral.com)

For both types of networks, the abstract network model can be set-up and edited via a Network Composer and input masks (see Figure 2 ) or, alternatively, via ASCII (text) files. (biomedcentral.com)

The endocytic pathway is the gateway between cells and their environment, and promotes diverse events such as nutrient uptake and cell migration. (royalsociety.org)

As a fundamental step, CNA facilitates the construction of network projects which can represent either a mass-flow (stoichiometric, metabolic) or a signal-flow (signal transduction/regulatory) network. (biomedcentral.com)

Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. (mdpi.com)
Functionally, QXHC candidate targets were significantly associated with several biological pathways, such as VEGF and Chemokine signaling pathways, Alanine/aspartate/glutamate metabolism, Long-term depression and T/B cell receptor signaling pathway. (biomedcentral.com)
This novel and scientific network pharmacology-based study holistically deciphers that the pharmacological mechanisms of QXHC in the treatment of menstrual disorders may be associated with its involvement into hemopoiesis, analgesia, nutrients absorption and metabolism, mood regulation, as well as immune modulation. (biomedcentral.com)
Based on the size of the genome-scale metabolic reconstruction and extent of validated predictions this model represents the most comprehensive up-to-date effort to catalogue methanogenic metabolism. (biomedcentral.com)
Furthermore, it is increasingly becoming apparent that archaeal metabolism has significant implications to the earth's climate [ 21 ] thus motivating the need to globally assess their true metabolic capabilities by reconstructing high quality metabolic models. (biomedcentral.com)

We are honored to host MPA 2023 in Asia for the first time, providing a memorable experience as we come together to study metabolic modeling and digital bio applications. (skku.edu)
MPA 2023 will serve as a platform for the exchange of knowledge and exploration of groundbreaking and translational research in systems/synthetic biology and metabolic pathway analysis. (skku.edu)
MPA 2023 is the ninth in the biennial series that integrates a highly interdisciplinary group of international biologists, computer scientists, engineers, and mathematicians for four days of discussions focused on state-of-the-art advances in network analysis methodology, theory, and applications. (skku.edu)

Recent multi-omics studies have revealed the heterogeneity and complexity of tumor features such as their genetic mutations, transcriptome, proteins, and signaling pathways. (rsc.org)
Cellular proteostasis involves the coordinated and compensatory action of pathways that control biogenesis, folding, trafficking and breakdown of proteins allowing the cell to adapt to physiological or pathological environmental changes. (elifesciences.org)
2010. The twin arginine protein transport pathway exports multiple virulence proteins in the plant pathogen Streptomyces scabies . (hutton.ac.uk)

There exists at least forty completed bacterial and thirteen eukaryotic metabolic reconstructions with many more under development [ 1 ]. (biomedcentral.com)

Over the last 15 years I have developed a research pathway in auxin biosynthesis going back to my degree and PhD work at the Technical University of Munich where I studied the nitrilase pathway in maize auxin biosynthesis and maize tryptophan synthase complex. (brookes.ac.uk)
Based on this work I won a fellowship from the Korean Federation of Science and Technology Societies to investigate the subcellular localisation of maize auxin biosynthesis at Dankook University in Seoul which lead to a publication that showed for the first time that both steps of the TAA/YUC pathway of auxin biosynthesis can be ER-localised. (brookes.ac.uk)

Different visualization features (e.g. pie-nodes, edge-pie matrix, etc.) aid in easy identification of the key nodes/interactions and their significance across the compared networks. (biomedcentral.com)
Gut microorganisms are the source of many bioactive products that play key functions in human host pathways and microbe-microbe interactions [2]. (deepdyve.com)
However, building dynamic models with high predictive power requires an amount of reliable quantitative data which is often not available in large-scale networks with hundreds of players and interactions. (biomedcentral.com)
We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)
Program access grant to the STFC Harwell Laser Facility 'The Plant Cell Initiative: Protein interactions in the higher plant secretory pathway' 2017-2021 (approximate value of £200K). (brookes.ac.uk)

The data suggest the therapeutic efficacy of BT2 may be attributable to the well-documented effects of mitochondrial uncoupling in alleviating cardiovascular and metabolic disease. (biomed.news)
Dysregulated mitochondrial dynamics respond rapidly to metabolic cues, and are linked to the initiation and progression of diverse human cancers. (biomed.news)
Based the dual action of OA in metabolic regulation and mitochondrial dynamics, further results revealed that mitochondrial functional status and spare respiratory capacity (SRC) of cancer cells had a close correlation with mitochondrial metabolic plasticity, and played important roles in the susceptibility to cancer therapy aiming at glucose restriction. (biomed.news)
Thus, inhibiting mitochondrial fusion breaks mitochondrial metabolic plasticity and increases cancer cell susceptibility to glucose restriction therapy. (biomed.news)
Collectively, these finding indicate that combining a GLUT1 inhibitor with a mitochondrial fusion inhibitor can work synergistically in cancer therapy and, more broadly, suggest that the incorporations of mitochondrial dynamics and metabolic regulation may become the targetable vulnerabilities bypassing the genotypic heterogeneity of multiple malignancies. (biomed.news)

The dynamic behavior of metabolic networks is governed by numerous regulatory mechanisms, such as reversible phosphorylation, binding of allosteric effectors or temporal gene expression, by which the activity of the participating enzymes can be adjusted to the functional requirements of the cell. (mpg.de)
Our results demonstrate mechanisms that can be used to switch between extensile and contractile stresses, as well as a range of new dynamical pathways and structures that are reminiscent of those observed in equilibrium amphiphilic systems. (aps.org)
Elevated levels of branched chain amino acids (BCAAs) and branched-chain α-ketoacids (BCKAs) are associated with cardiovascular and metabolic disease, but the molecular mechanisms underlying a putative causal relationship remain unclear. (biomed.news)
Therefore, we attempted to identify the critical pathogenic HCM pathways and pathophysiological mechanisms associated with non-myocyte mutations [ 12 ]. (biomedcentral.com)

Weighted correlation network analysis, also known as weighted gene co-expression network analysis (WGCNA), is a widely used data mining method especially for studying biological networks based on pairwise correlations between variables. (wikipedia.org)
The tool also allows one to perform network comparisons on the basis of neighbourhood architecture of constituent nodes and community compositions, a feature particularly useful while analyzing biological networks. (biomedcentral.com)
Recent emergence of systems biology has brought biological networks into focus. (biomedcentral.com)
Systems biology aims at a holistic analysis of biological networks. (biomedcentral.com)
A key SB tool, the reconstruction of biological networks, represents an emerging field, undergoing explosive expansion, and will likely enable efficient mapping of gene onto function. (deepdyve.com)
In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. (researchgate.net)
Biological networks are often used to identify active subnetworks (ASNs) of the diseases from the expression profiles to understand the reason behind the observed changes. (biomedcentral.com)

Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. (leibniz-fli.de)

Using these models they can measure and test for generalized patterns in the structure of real food web networks. (wikipedia.org)
However, the number of empirical studies on community webs is on the rise and the mathematical treatment of food webs using network theory had identified patterns that are common to all. (wikipedia.org)
In addition to comparison of graph properties/metrics in form of tables or charts, identifying and comprehending the patterns of variations across different networks becomes several folds easier if provisions exist for visual comparisons, such as creation of graph layouts, overlaying of multiple networks, and interactive analysis of graph components. (biomedcentral.com)
Oxidative stress is involved in the modulation of gene expression patterns and metabolic activities, characterized by the disruption of redox homeostasis 7 . (nature.com)
Metabolic state, insulin levels and glucose administration interact in their effects on brain activation patterns. (frontiersin.org)
The model also correctly recapitulates metabolic pathway usage patterns of M. acetivorans such as the indispensability of flux through methanogenesis for growth on acetate and methanol and the unique biochemical characteristics under growth on carbon monoxide. (biomedcentral.com)

It allows one to define modules (clusters), intramodular hubs, and network nodes with regard to module membership, to study the relationships between co-expression modules, and to compare the network topology of different networks (differential network analysis). (wikipedia.org)
We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. (biomedcentral.com)
QXHC candidate targets were also identified via calculating the topological feature values of nodes in the network. (biomedcentral.com)

Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. (biomedcentral.com)

An interaction network using links between QXHC putative targets and the known therapeutic targets of menstrual disorders was constructed. (biomedcentral.com)
Following the calculation of topological features of QXHC putative target-known therapeutic target of menstrual disorder network, 66 QXHC candidate targets for the treatment of menstrual disorders were identified. (biomedcentral.com)

To study the interplay of metabolic state (hungry vs. satiated) and glucose administration (including hormonal modulation) on brain function, resting-state functional magnetic resonance imaging (rs-fMRI) and blood samples were obtained in 24 healthy normal-weight men in a repeated measurement design. (frontiersin.org)
To avoid these disadvantages in the present investigation, we used resting-state fMRI in order to reveal potential links between whole brain activity and insulin and glucose levels in different metabolic states. (frontiersin.org)
Several studies using rs-fMRI revealed associations of insulin or glucose levels with the functional connectivity (FC) of particular brain networks or brain sites that are related to homeostatic regulation but not without contradictions. (frontiersin.org)

Previous studies have identified many immune pathways which are consistently altered in humans and model organisms as they age. (biomedcentral.com)

Although WGCNA incorporates traditional data exploratory techniques, its intuitive network language and analysis framework transcend any standard analysis technique. (wikipedia.org)
Since it uses network methodology and is well suited for integrating complementary genomic data sets, it can be interpreted as systems biologic or systems genetic data analysis method. (wikipedia.org)
By selecting intramodular hubs in consensus modules, WGCNA also gives rise to network based meta analysis techniques. (wikipedia.org)
Weighted correlation network analysis can be attractive for the following reasons: The network construction (based on soft thresholding the correlation coefficient) preserves the continuous nature of the underlying correlation information. (wikipedia.org)
Network visualization and analysis tools aid in better understanding of complex biological systems. (biomedcentral.com)
With increasing interests in systems biology, tools specialized for analysis of complex metabolic networks (represented in information rich graph formats like SBML) has also been developed [ 15 ]. (biomedcentral.com)
An important class of methods in Systems Biology deals with structural or topological (parameter-free) analysis of cellular networks. (biomedcentral.com)
Herein we introduce CellNetAnalyzer , a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks. (biomedcentral.com)
The particular strengths of CellNetAnalyzer are methods for functional network analysis, i.e. for characterising functional states, for detecting functional dependencies, for identifying intervention strategies, or for giving qualitative predictions on the effects of perturbations. (biomedcentral.com)
CellNetAnalyzer extends its predecessor FluxAnalyzer (originally developed for metabolic network and pathway analysis) by a new modelling framework for examining signal-flow networks. (biomedcentral.com)
Two of the novel methods implemented in CellNetAnalyzer are discussed in more detail regarding algorithmic issues and applications: the computation and analysis (i) of shortest positive and shortest negative paths and circuits in interaction graphs and (ii) of minimal intervention sets in logical networks. (biomedcentral.com)
CellNetAnalyzer provides a single suite to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks in a user-friendly environment. (biomedcentral.com)
It provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis. (biomedcentral.com)
CellNetAnalyzer (CNA) is a graphical user interface for MATLAB providing a comprehensive toolbox for structural and functional analysis of different types of cellular networks. (biomedcentral.com)
CNA extends its predecessor FluxAnalyzer , originally developed for metabolic network analysis [ 7 ], by new methods for signalling and regulatory networks, i.e. for networks where signal flows are dominating (in contrast to mass flows in metabolic networks). (biomedcentral.com)
3 cows with MP 2-3 as background using DESeq2 followed by weighted gene co-expression network analysis (WGCNA). (biomedcentral.com)
We think that the proposed method represents an important intermediate step on the long way from topological network analysis to detailed kinetic modeling of complex metabolic networks. (mpg.de)
Greetings and a warm welcome to the 9th Metabolic Pathway Analysis (MPA) International Conference. (skku.edu)
Weighted gene coexpression network analysis (WGCNA) of 1570 DE-lncRNAs between WT and ZBED6 KO pigs was used to define the following six lncRNA modules specific to different tissues: skeletal muscle, heart, lung, spleen, kidney and liver modules. (biomedcentral.com)
A fast and accurate algorithm for comparative analysis of metabolic pathways. (leibniz-fli.de)
Comparative analysis and unification of domain-domain interaction networks. (leibniz-fli.de)

Noncommunicable diseases, including cardiovascular, metabolic and respiratory diseases, among others, are the major medical challenge of the 21st century. (ersjournals.com)

Therefore, the reconstruction of archaeal methanogen metabolic models could help paint a more complete picture of life's metabolic processes. (biomedcentral.com)

Moreover, our approach allows to differentiate quantitatively between metabolic states related to senescence and metabolic collapse of the human erythrocyte. (mpg.de)

Network representations have been widely used in physics and social science for decades, and are now among the most frequently used tools in systems biology. (biomedcentral.com)
A new field of research, known as systems biology if applied to model systems or network medicine if applied to human beings, has emerged over the past decade or so, to address biological complexity in a holistic, integrated way. (ersjournals.com)
In this State of the Art review we present the basic concepts of systems biology, use some examples to illustrate the potential of network medicine to address complex medical problems, and review some recent publications that show how a systems-based research strategy can contribute to improve our understanding of multimorbidity and age-related respiratory diseases. (ersjournals.com)

To explore the possible dynamic behavior of metabolic networks in cases of lacking or incomplete enzyme-kinetic information, we present a computational approach based on structural kinetic modeling. (mpg.de)

There is a vast literature on dependency networks, scale free networks and coexpression networks. (wikipedia.org)

This can limit their ability to find the meaningful ASNs when using integrated networks having comprehensive information than the traditional protein-protein interaction networks. (biomedcentral.com)
PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks. (leibniz-fli.de)

The linkages in a food web illustrate the feeding pathways, such as where heterotrophs obtain organic matter by feeding on autotrophs and other heterotrophs. (wikipedia.org)

Our findings show that allosteric enzyme regulation significantly enhances the stability of the network and extends its potential dynamic behavior. (mpg.de)
Metabolic adaptations significantly contribute to tumor development and escape from tissue homeostatic defenses. (biomed.news)

Also module preservation statistics allow one to study differences between the modular structure of networks. (wikipedia.org)
MPA is a leading meeting for the scientific community analyzing topological structure-function relationships of metabolic networks to study fundamentals of biology and biotechnological applications. (skku.edu)

In this review, we aim to improve the understanding of challenges in biomedical research and establish a common ground between clinicians and systems biologists to further promote the application of network biology in translational medicine. (biomedcentral.com)

Structural or qualitative (parameter-free) models relying solely on the often well-known network structure provide an alternative approach still capable to gain useful insights in the functioning of these networks [ 3 - 6 ]. (biomedcentral.com)
We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
The authors also considered the principle of transition to topological thermal models of structural elements of an optoelectronic device. (hse.ru)
BT2 administration is protective in various rodent models of heart failure and metabolic disease, but confoundingly, targeted ablation of Bckdk in specific tissues does not reproduce the beneficial effects conferred by pharmacologic inhibition. (biomed.news)

In particular, weighted correlation networks were developed in joint discussions with cancer researchers Paul Mischel, Stanley F. Nelson, and neuroscientists Daniel H. Geschwind, Michael C. Oldham (according to the acknowledgement section in). (wikipedia.org)
citation needed] A weighted correlation network can be interpreted as special case of a weighted network, dependency network or correlation network. (wikipedia.org)
For example, weighted correlation networks that are constructed on the basis of correlations between numeric variables do not require the choice of a hard threshold. (wikipedia.org)
Weighted correlation networks facilitate a geometric interpretation based on the angular interpretation of the correlation, chapter 6 in. (wikipedia.org)
Weighted networks and correlation networks can often be approximated by "factorizable" networks. (wikipedia.org)
Therefore, weighted (correlation) networks allow for a parsimonious parametrization (in terms of modules and module membership) (chapters 2, 6 in ) and. (wikipedia.org)
Firstly, normal and ccRCC PPI network were inferred and reweighted based on Pearson correlation coefficient (PCC). (hindawi.com)

Finally, we identified 76 therapeutic agents, 152 miRNAs targets, and 91 TFs regulatory networks. (nature.com)
So far, software tools providing such methods for both mass-flow (metabolic) as well as signal-flow (signalling and regulatory) networks are lacking. (biomedcentral.com)

In addition, unique biochemical properties such as broad substrate specificity, participation of novel coenzymes in the methanogenesis pathways and the presence of unique lipids in their cell wall set these organisms apart from the bacterial and eukaryotic branches of life [ 28 ]. (biomedcentral.com)

This process relies on previously developed computational tools developed in our group to correct growth prediction inconsistencies with in vivo data sets and rectify topological inconsistencies in the model. (biomedcentral.com)

Interaction networks are a convenient way of representing the complex nature of multi-component systems. (biomedcentral.com)
Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. (leibniz-fli.de)

NASCENT: An automatic protein interaction network generation tool for non-model organisms. (leibniz-fli.de)

Network representation is frequently used to capture the presence of these molecules as well as their relationship. (biomedcentral.com)
Delineating the pathogenesis of ccRCC by investigating the gene and epigenetic changes and their effects on key molecules and their respective biologic pathways is of crucial importance for the improvement of current diagnostics, prognostics, and drug development [ 4 ]. (hindawi.com)

Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. (biomedcentral.com)
Tanshinone IIA targeting cell signaling pathways: a plausible paradigm for cancer therapy. (ncbs.res.in)
Cancer cells with healthy mitochondria and high SRC exhibit greater metabolic flexibility and higher resistance to GLUT1 inhibitors. (biomed.news)

To demonstrate the utility of CompNet, we have compared a (time-series) human gene-expression dataset, post-infection by two strains of Mycobacterium tuberculosis , overlaid on the human protein-protein interaction network. (biomedcentral.com)

We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. (nature.com)

Thanks to the natural inertia of heat exchanges, these networks can offer flexibility. (lu.se)

Triangle network motifs predict complexes by complementing high-error interactomes with structural information. (leibniz-fli.de)

Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. (biomedcentral.com)
From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases. (biomedcentral.com)

There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)
However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones. (researchgate.net)

First, one defines a gene co-expression similarity measure which is used to define the network. (wikipedia.org)
Although many available network comparison methods exist, which employ techniques like network alignment and querying to compute pair-wise similarity between selected networks, most of them have limited features with respect to interactive visual comparison of multiple networks. (biomedcentral.com)
These tools employ different algorithms to compute pair wise similarity between selected networks/paths. (biomedcentral.com)

In this paper, we present CompNet - a graphical user interface based network comparison tool, which allows visual comparison of multiple networks based on various network metrics. (biomedcentral.com)

Furthermore, to understand the differences in behaviour of system(s) under various environmental conditions (e.g. stress, infection), comparing multiple networks becomes necessary. (biomedcentral.com)
Such comparisons between multiple networks may help in asserting causation and in identifying key components of the studied biological system(s). (biomedcentral.com)
Although some of these tools like MIMO [ 15 ], have options for graphical visualization of outputs, in general, the network alignment and querying methods do not provide any dedicated module/options for visual comparison of multiple networks on a single canvas. (biomedcentral.com)

But it has been noticed that PPI data are often associated with high false positive and false negative rates due to the limitations of the associated experimental techniques and the dynamic nature of protein interaction maps, which may have a negative impact on the performance of complex discovery algorithms [ 11 ]. (hindawi.com)

Anatomy4

Organisms15

Chemicals and Drugs18

Analytical, Diagnostic and Therapeutic Techniques and Equipment21

Phenomena and Processes47

Disciplines and Occupations12

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Humanities1

Information Science22

Health Care8

Genes24

Genome-Scale Metabolic Model1

Abstract1

Endocytic pathway1

Signal transduction1

Metabolism5

20233

Proteins3

Reconstructions1

Biosynthesis2

Interactions6

Mitochondrial5

Mechanisms4

Biological networks7

Characterization1

Patterns6

Nodes3

Mathematical1

Putative2

Glucose3

Humans1

Analysis21

Cardiovascular1

Reconstruction1

Quantitatively1

Systems biology3

Kinetic1

Coexpression1

Protein-protein interaction2

Illustrate1

Significantly2

Study2

Translational1

Models4

Correlation7

Regulatory2

Bacterial1

Prediction1

Interaction networks3

Model organisms1

Molecules2

Cancer3

Human1

Microbiome1

Flexibility1

Predict1

Biology2

Mutations2

Similarity3

Graphical user inte1

Multiple3

Complex1