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Visualizing regulatory interactions in metabolic networks

Stephan Noack, Aljoscha Wahl, Ermir Qeli, Wolfgang Wiechert
2007 BMC Biology  
Results: The visualization of such interactions in a given metabolic network is based on a novel concept defining the regulatory strength (RS) of effectors regulating certain reaction steps.  ...  Direct visualization of data sets in the context of biochemical network drawings is one of the most appealing approaches in the field of data evaluation within systems biology.  ...  The visualization of regulatory interactions in a given metabolic network is based on a novel concept defining the RS of effectors regulating certain reaction steps.  ... 
doi:10.1186/1741-7007-5-46 pmid:17939866 pmcid:PMC2216428 fatcat:5rhzroiigvcpxkbqox4wkrpxg4

Visualizing regulatory interactions in metabolic networks

Stephan Noack, Aljoscha Wahl, Marco Oldiges, Wolfgang Wiechert
2007 BMC Systems Biology  
In this contribution we present a general definition for the Regulatory Strength (RS) of an effector interaction and its application to a relevant biochemical network model.  ...  One numerical RS value is associated to any effector edge contained in the network. Thus it is possible to visualize RS's directly in the network context.  ...  In this contribution we present a general definition for the Regulatory Strength (RS) of an effector interaction and its application to a relevant biochemical network model.  ... 
doi:10.1186/1752-0509-1-s1-p5 fatcat:ucju5iw65zeslp7w6tvhnz6aem

MetNet: Software to Build and Model the Biogenetic Lattice ofArabidopsis

Eve Syrkin Wurtele, Jie Li, Lixia Diao, Hailong Zhang, Carol M. Foster, Beth Fatland, Julie Dickerson, Andrew Brown, Zach Cox, Dianne Cook, Eun-Kyung Lee, Heike Hofmann
2003 Comparative and Functional Genomics  
The software is designed to enable the biologist to visualize, statistically analyse and model a metabolic and regulatory network map ofArabidopsis, combined with gene expression profiling data.  ...  It contains a JAVA interface to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases (TAIR, KEGG, BRENDA) and  ...  Many gaps remain in our understanding of the interactions in the metabolic and regulatory network map.  ... 
doi:10.1002/cfg.285 pmid:18629120 pmcid:PMC2447407 fatcat:fx32ghasijgklhfowqqguacqqq

Visualizing Temporal Dynamics at the Genomic and Metabolic Level

Romain Bourqui, Michel A. Westenberg
2009 2009 13th International Conference Information Visualisation  
Our application can (i) visualize the data from time series experiments in the context of a regulatory network and a metabolic network; (ii) identify and visualize active regulatory subnetworks from the  ...  We present an application for integrated visualization of gene expression data from time series experiments in gene regulation networks and metabolic networks.  ...  Regulatory network visualization A gene regulatory network is represented by a graph, in which nodes represent genes, and edges represent interactions between a gene product (a regulator protein) and its  ... 
doi:10.1109/iv.2009.41 dblp:conf/iv/BourquiW09 fatcat:gz35nbw5qbfpjg3vlxgrzqjapi

BioNetLink - An Architecture for Working with Network Data

Matthias Klapperstück, Falk Schreiber
2014 Journal of Integrative Bioinformatics  
In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction  ...  and gene regulatory networks in an example.  ...  The visualizer thereby uses the layout found in the metabolic data model and does a new force directed layout on the extracted regulatory network.  ... 
doi:10.1515/jib-2014-241 fatcat:jxotdmvpqrdd3iii4frlpnekom

BioNetLink - an architecture for working with network data

Matthias Klapperstück, Falk Schreiber
2014 Journal of Integrative Bioinformatics  
In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction  ...  and gene regulatory networks in an example.  ...  The visualizer thereby uses the layout found in the metabolic data model and does a new force directed layout on the extracted regulatory network.  ... 
doi:10.2390/biecoll-jib-2014-241 pmid:24980619 fatcat:gfmxqpvgujcwfcxnt52mdsllru

2.5D Visualisation of Overlapping Biological Networks

David C.Y. Fung, Seok-Hee Hong, Dirk Koschützki, Falk Schreiber, Kai Xu
2008 Journal of Integrative Bioinformatics  
AbstractBiological data is often structured in the form of complex interconnected networks such as protein interaction and metabolic networks.  ...  Using three biological datasets, we evaluate our visualisation design with the aim to test whether overlapping networks can support the visual analysis of heterogeneous and yet interconnected networks.  ...  However, in such integrated networks, the different modes of interaction such as protein interaction and metabolism are not visually separated anymore and therefore it is not possible to investigate and  ... 
doi:10.1515/jib-2008-90 fatcat:dlcntj7a5newxc7a73dl64yoyi

ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks

Johannes Klein, Stefan Leupold, Richard Münch, Claudia Pommerenke, Thorsten Johl, Uwe Kärst, Lothar Jänsch, Dieter Jahn, Ida Retter
2008 Nucleic Acids Research  
ProdoNet is a web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks.  ...  Furthermore, the co-occurrence of genes of interest in gene expression profiles can be added to the visualization of the global network.  ...  ACKNOWLEDGEMENTS We would like to thank Hedwig Schrader for excellent technical assistance and Dr Max Schobert for fruitful discussions on regulatory networks in P. aeruginosa.  ... 
doi:10.1093/nar/gkn217 pmid:18440972 pmcid:PMC2447764 fatcat:3dgjac37sbacfb4ubi6drgxfla

PaVESy: Pathway Visualization and Editing System

A. Ludemann, D. Weicht, J. Selbig, J. Kopka
2004 Bioinformatics  
The database design allows storage of biological objects, such as metabolites, proteins, genes and respective relations, which are required to assemble metabolic and regulatory biological interactions.  ...  We created editing and visualization tools for navigation in and visualization of the database content.  ...  for allowing access to the BRENDA collection (http://www.brenda.uni-koeln.de) and acknowledge the Kyoto Encyclopedia of Genes and Genomes (http://www.genome.ad.jp/kegg) for providing public access to metabolic  ... 
doi:10.1093/bioinformatics/bth278 pmid:15105280 fatcat:pv66ynigszeyjojb56yqxvna7m

Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context

M. A. Westenberg, S. A. F. T. van Hijum, O. P. Kuipers, J. B. T. M. Roerdink
2008 Computer graphics forum (Print)  
We present an application for integrated visualization of genome expression and network dynamics in both regulatory networks and metabolic pathways.  ...  Our application can (i) visualize the data from time series experiments in the context of a regulatory network and KEGG metabolic pathways; (ii) identify and visualize active regulatory subnetworks from  ...  Here, we present an application for integrated visualization of genome expression and network dynamics in both regulatory networks and metabolic pathways.  ... 
doi:10.1111/j.1467-8659.2008.01221.x fatcat:3j5o27gqazdjhnyrhhsxf6hi3a

BiNA: A Visual Analytics Tool for Biological Network Data

Andreas Gerasch, Daniel Faber, Jan Küntzer, Peter Niermann, Oliver Kohlbacher, Hans-Peter Lenhof, Michael Kaufmann, Alexey Porollo
2014 PLoS ONE  
Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering  ...  Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts.  ...  Another essential difference is BiNA's network visualization model, which is based on hierarchical graphs and focuses comprehensive, dynamic, and interactive visualizations for metabolic, regulatory, and  ... 
doi:10.1371/journal.pone.0087397 pmid:24551056 pmcid:PMC3923765 fatcat:m6mtpy5cr5f75ezss43tf466li

Analysis of Pan-Omics Data in Human Interactome Network (APODHIN) [article]

Nupur Biswas, Krishna Kumar, Sarpita Bose, Raisa Bera, Saikat Chakrabarti
2020 bioRxiv   pre-print
APODHIN works on a meta-interactome networks consisting of human protein-protein interactions, miRNA-target gene regulatory interactions, and transcription factor-target gene regulatory relationships,  ...  In its second module, APODHIN attempts to identify cross pathway regulatory and protein-protein interaction (PPI) links connecting signaling proteins, transcription factors, and miRNAs to metabolic enzymes  ...  These paths are shown both in tabular and interactive 3D network visualization.  ... 
doi:10.1101/2020.04.18.048207 fatcat:g6oulznrnnb63iezjtqhqnog2m

Fuzzy modeling of metabolic maps in MetNetDB

J.A. Dickerson, Pan Du, E. Wurtele, Jie Li
2004 IEEE Annual Meeting of the Fuzzy Information, 2004. Processing NAFIPS '04.  
FCModeler, a publicly available software package is designed to enable the biologist to visualize and model metabolic and regulatory network maps in plants.  ...  It links to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases and input from biologists in their area of expertise  ...  Thank you to our Metabolic Networking project collaborators: Dr. Dianne Cook, and Dr. Carolina Cruz-Neira.  ... 
doi:10.1109/nafips.2004.1336272 fatcat:fb5takeg4fhrvocgde6x4kbhbu

An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice

Lili Liu, Qian Mei, Zhenning Yu, Tianhao Sun, Zijun Zhang, Ming Chen
2013 Journal of Integrative Bioinformatics  
to phenotype through gene regulatory networks (GRNs), protein-protein interactions (PPIs) and molecular pathways.  ...  Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology.  ...  In the study of genotypephenotype relationship, more and more attention is paid to the dynamic path from genotypes to phenotypes through gene regulatory networks, protein interactions and metabolic networks  ... 
doi:10.2390/biecoll-jib-2013-223 pmid:23563093 fatcat:dfetaonsfbfoteq3vaisfrbzga

An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice

Lili Liu, Qian Mei, Zhenning Yu, Tianhao Sun, Zijun Zhang, Ming Chen
2013 Journal of Integrative Bioinformatics  
to phenotype through gene regulatory networks (GRNs), protein-protein interactions (PPIs) and molecular pathways.  ...  SummaryUnderstanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology.  ...  In the study of genotypephenotype relationship, more and more attention is paid to the dynamic path from genotypes to phenotypes through gene regulatory networks, protein interactions and metabolic networks  ... 
doi:10.1515/jib-2013-223 fatcat:lvpladsbifdpjpn232ng5fsimi
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