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Metabolic network visualization eliminating node redundance and preserving metabolic pathways

Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Auber, Patrick Mary, Marie-France Sagot, Fabien Jourdan
2007 BMC Systems Biology  
Metabolic network visualization eliminating node redundance and preserving metabolic pathways.  ...  Results: We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways.  ...  Acknowledgements The work presented in this paper was funded in part by the ACI Nouvelles Interfaces des Mathématiques (project p-vert) of the French Ministry of Research, by the ARC (project IBN) from the INRIA and  ... 
doi:10.1186/1752-0509-1-29 pmid:17608928 pmcid:PMC1934383 fatcat:7bm57u4rujeobhwjscmucht52a

Development of an Algorithm for Reconstructing a Comprehensive Pathway Model: Application to Saccharomyces cerevisiae

Itaru Takeda, Masayuki Machida, Sachiyo Aburatani
2015 Journal of Biomedical Science and Engineering  
Recently, an abundance of knowledge about metabolic pathways has been accumulated in metabolic pathway databases, such as BioCyc and KEGG.  ...  From this model, the pathways among enzymes that contributed to galactose metabolism were explored.  ...  Acknowledgements This work was supported by a grant from the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial, from the Ministry of Economy, Trade and  ... 
doi:10.4236/jbise.2015.88047 fatcat:vcrseuk4tjhcdnnbm6pqegmvnq

Computationally efficient measure of topological redundancy of biological and social networks

Réka Albert, Bhaskar DasGupta, Rashmi Hegde, Gowri Sangeetha Sivanathan, Anthony Gitter, Gamze Gürsoy, Pradyut Paul, Eduardo Sontag
2011 Physical Review E  
, metabolic and social interaction networks.  ...  , (3) the topological redundancy of the C. elegans metabolic network is largely due to its inclusion of currency metabolites, and (4) the redundancy of signaling networks is highly (negatively) correlated  ...  CCF-0643529 and Eduardo Sontag was supported by National Institutes of Health Grant No. 1R01GM086881 during this work.  ... 
doi:10.1103/physreve.84.036117 pmid:22060466 fatcat:rsoe6g3oajbqvaoyjmdbnkliqa

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database

Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis, Fragiskos N Kolisis
2009 BMC Bioinformatics  
Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope.  ...  The KEGG Pathway database is a valuable collection of metabolic pathway maps.  ...  Part of this research has been cofunded by the EU/FP7/ICT-2007.4.4 Intelligent Content and Semantics, "e-Laboratory for Interdisciplinary Collaborative Research in Data Mining and Data-Intensive Sciences-e-LICO  ... 
doi:10.1186/1471-2105-10-324 pmid:19814801 pmcid:PMC2764712 fatcat:ecs5gu7kyraotatdqtepa4kevu

Network motif frequency vectors reveal evolving metabolic network organisation

Nicole Pearcy, Jonathan J. Crofts, Nadia Chuzhanova
2015 Molecular Biosystems  
At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models.  ...  Acknowledgement We thank Kazuhiro Takemoto for generously providing the metabolic data used in this study and for a number of useful discussions.  ...  4-node motifs, the metabolic network of E. coli is mapped into a 212-dimensional Euclidean space.  ... 
doi:10.1039/c4mb00430b pmid:25325903 fatcat:yfgrn4st3vcxlbshfilatfkfqe

Role of tryptophan-metabolizing microbiota in mice diarrhea caused by Folium sennae extracts

Chenyang Zhang, Haoqing Shao, Dandan Li, Nenqun Xiao, Zhoujin Tan
2020 BMC Microbiology  
Combining PPI network analysis, cytochrome P450 enzymes metabolism was the main signaling pathway of diarrhea caused by Folium sennae.  ...  Folium sennae targeted cytochrome P450 3A4 to alter intestinal bacterial characteristic and intervene the tryptophan metabolism of intestinal microbiota, such as Streptococcus, Sutterella and Dorea, which  ...  HS and NX supervised the research work and guided the experimental design. CZ and DL provided the suggestion of the research work. ZC prepared the manuscript.  ... 
doi:10.1186/s12866-020-01864-x pmid:32600333 fatcat:4shfhpk6inev5lovt6xsuaxm3a

Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis

Oriol Güell, Francesc Sagués, M. Ángeles Serrano, Jens Nielsen
2014 PLoS Computational Biology  
We unravel how functional plasticity and redundancy are essential mechanisms underlying the ability to survive of metabolic networks.  ...  When comparing E. coli and Mycoplasma pneumoniae, we find that the metabolic networks of the two organisms exhibit a large difference in the relative importance of plasticity and redundancy which is consistent  ...  Acknowledgments We thank Judith Wodke for solving doubts about the network of M. pneumoniae. Author Contributions Analyzed the data: OG FS MAS.  ... 
doi:10.1371/journal.pcbi.1003637 pmid:24854166 pmcid:PMC4031049 fatcat:gj6evp4zwzaplcwfsh6qsfup7q

Molecular Evolution, Networks in [chapter]

Andreas Wagner
2009 Encyclopedia of Complexity and Systems Science  
, and metabolic networks.  ...  For example, metabolic networks can be represented as graphs whose nodes are enzymes and metabolites. Two nodes are connected if they participate in the same chemical reactions.  ... 
doi:10.1007/978-0-387-30440-3_336 fatcat:rl5u3k5nwbhwbopik7e6tg446m

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

J. F. Moxley, M. C. Jewett, M. R. Antoniewicz, S. G. Villas-Boas, H. Alper, R. T. Wheeler, L. Tong, A. G. Hinnebusch, T. Ideker, J. Nielsen, G. Stephanopoulos
2009 Proceedings of the National Academy of Sciences of the United States of America  
Previous in silico attempts to address this gap included metabolic network and regulatory on/off switch models for growth and viability prediction (8, 9)  ...  The model provides evidence of general biological principles: rewiring of metabolic flux (i.e., use of different reaction pathways) by transcriptional regulation and metabolite interaction density (i.e  ...  We thank Ryan Kelley, Tong Ihn Lee, Scott McCuine, Chris Workman, Jose Aleman, Richard Young, and Gerald Fink for advice on experimental design and analysis.  ... 
doi:10.1073/pnas.0811091106 pmid:19346491 pmcid:PMC2672541 fatcat:ynqb5ouarva3rdqpebvlowjm3m

Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

John A. Gerlt
2017 Biochemistry  
similarity networks to visualize and analyze sequence−function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks  ...  to visualize and analyze the genome context in microbial and fungal genomes.  ...  Several options are provided, including (1) eliminating overrepresented phylogenetically related subspecies from the input SSN to reduce redundancy in the GNN and (2) using a user-defined "whitelist" of  ... 
doi:10.1021/acs.biochem.7b00614 pmid:28826221 pmcid:PMC5569362 fatcat:t6awgzfi6jdafp62pfzxfl2t5e

Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania [article]

Nutan Chauhan, Shailza Singh
2019 bioRxiv   pre-print
The analyses helped us to identify the importance of several nodes and detect sub-networks.  ...  Our results revealed several key high curvature nodes (metabolites) belonging to common yet crucial metabolic, thus, maintaining the integrity of the network which signifies its robustness.  ...  Importantly, our analyses have pointed out several central nodes belonging to very common yet crucial metabolic pathways those include glycolysis, glyoxalase pathway, and T[SH] 2 metabolism pathways (  ... 
doi:10.1101/512277 fatcat:76e3pcxeqrhoxbpreo66tn6qvi

Influence of pathway topology and functional class on the molecular evolution of human metabolic genes

Ludovica Montanucci, Hafid Laayouni, Begoña Dobon, Kevin L. Keys, Jaume Bertranpetit, Juli Peretó, Christian Schönbach
2018 PLoS ONE  
These results show how functional and topological characteristics of metabolic pathways contribute to shape the patterns of evolutionary pressures driven by natural selection and how pathway network structure  ...  Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection.  ...  Acknowledgments Authors would like to acknowledge Dr Peter Karp and Dr Ron Caspi for their support and help with data in HumanCyc database.  ... 
doi:10.1371/journal.pone.0208782 pmid:30550546 pmcid:PMC6294346 fatcat:hphv4hryovdclac4do55znmmwy


2012 Journal of Bioinformatics and Computational Biology  
We also present a computational performance evaluation of the SMDA tool against a mammalian metabolic network database.  ...  In this paper, we present the steady-state metabolic network dynamics analysis (SMDA) approach in detail, together with its application in a cystic fibrosis study.  ...  Acknowledgments This research is supported by the National Science Foundation under grants DBI-0849956 and DBI-0743705, and the National Institute of Health under grant R01 GM088823.  ... 
doi:10.1142/s0219720012400033 pmid:22809304 pmcid:PMC4123123 fatcat:rodrqho7bbeofemqoerylaovzu

An Introduction to Metabolic Networks and Their Structural Analysis

V. Lacroix, L. Cottret, P. Thebault, M.-F. Sagot
2008 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We explain methods for acquiring data and reconstructing metabolic networks and review the various models that have been used for their structural analysis.  ...  There has been a renewed interest for metabolism in the computational biology community, leading to an avalanche of papers coming from methodological network analysis as well as experimental and theoretical  ...  tool in the Pathway Tools used to build, query, and visualize BioCyc-like databases [86] .  ... 
doi:10.1109/tcbb.2008.79 pmid:18989046 fatcat:iomp7dhnvndgtlwhpeyc4dnvoa

Revealing gene regulation and associations through biological networks

Christophe Liseron-Monfils, Doreen Ware
2015 Current Plant Biology  
In crop species, one aim of QTL analysis is to define genetic regions responsible for architectural and stress-related phenotypes, e.g., the response to water deficit and the efficiency of nitrogen use  ...  Such (re) discovery of lost alleles could help meet challenging breeding goals such as conferring tolerance to drought, salinity, and other stresses [1, 2] .  ...  On the other hand, one area in which inference networks seem to perform well is metabolic pathway prediction: factors involved in specialized metabolic pathways exhibit a high level of co-expression, suggesting  ... 
doi:10.1016/j.cpb.2015.11.001 fatcat:oz6mwmi6nrgnlgmnahp7bc7yim
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