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A logic-based diagram of signalling pathways central to macrophage activation

Sobia Raza, Kevin A Robertson, Paul A Lacaze, David Page, Anton J Enright, Peter Ghazal, Tom C Freeman
2008 BMC Systems Biology  
and logic-based pathway diagram of signalling cascades fundamental to macrophage activation using a current version of the EPN scheme.  ...  a pathway diagram based on published literature.  ...  Authors' contributions SR constructed the integrated pathway diagram, contributed to the development of the notation system, participated in the expression profiling and analysis, and helped to draft the  ... 
doi:10.1186/1752-0509-2-36 pmid:18433497 pmcid:PMC2383880 fatcat:n4qpohu7wvgsppuuj2nssp2et4

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

Sobia Raza, Neil McDerment, Paul A Lacaze, Kevin Robertson, Steven Watterson, Ying Chen, Michael Chisholm, George Eleftheriadis, Stephanie Monk, Maire O'Sullivan, Arran Turnbull, Douglas Roy (+3 others)
2010 BMC Systems Biology  
In an effort to better understand the molecular networks that underpin macrophage activation we have been assembling a map of relevant pathways.  ...  Conclusions: The pathway diagram is a navigable visual aid for displaying a consensus view of the pathway information available for these systems.  ...  MHC antigen presentation Cytokine Activation Pathways The diagram also describes a number of the main cytokine signalling systems active in macrophages.  ... 
doi:10.1186/1752-0509-4-63 pmid:20470404 pmcid:PMC2892459 fatcat:yg457jygdfa2xjhftsn2f4rzcu

Initial Analysis of Tumour Necrosis Factor alpha Promotor Activation by Interferon gamma using Boolean Logic Modelling

Wei Yuan Hsieh, Alexander Mazein, Steven Watterson, Douglas Roy, Peter Ghazal
2012 Figshare  
A report produced as part of the MSc in Genomics and Pathway Biology course at the Division of Pathway Medicine, University of Edinburgh. (http://www.ed.ac.uk/schools-departments/pathway-medicine).  ...  In an effort to describe and consolidate knowledge of pathways central to TNF-α activation by IFN-ɣ, we have constructed a pathway diagram based on published literature.  ...  of the pathway to reflect endogenous TNF-α activation in macrophage.  ... 
doi:10.6084/m9.figshare.105169.v1 fatcat:wuy6bpzevrf2ni5kho776ynwhm

The in silico macrophage: toward a better understanding of inflammatory disease

Peter Ghazal, Steven Watterson, Kevin Robertson, David C Kluth
2011 Genome Medicine  
Macrophages function as sentinel, cell-regulatory hubs capable of initiating, perpetuating and contributing to the resolution of an inflammatory response, following their activation from a resting state  ...  To investigate how programs of gene expression relate to the phenotypic attributes of the macrophage, the development of in silico modeling methods is needed.  ...  Acknowledgements This work was supported by the Wellcome Trust (WT066784) program grant and BBSRC to PG.  ... 
doi:10.1186/gm218 pmid:21349141 pmcid:PMC3092089 fatcat:z2sjufkuy5fu5dw3kkzzjmyrfq

Modeling of cell signaling pathways in macrophages by semantic networks

Michael Hsing, Joel L Bellenson, Conor Shankey, Artem Cherkasov
2004 BMC Bioinformatics  
We have applied a semantic network (SN) approach to develop and implement a model for cell signaling pathways.  ...  Conventionally, this information is stored in the form of pathway diagrams and can be characterized as highly "compartmental" (i.e. individual pathways are not connected into more general networks).  ...  behaviors of molecules depicted in conventional pathways and to reconstruct a cell signaling network of the human macrophage.  ... 
doi:10.1186/1471-2105-5-156 pmid:15494071 pmcid:PMC528732 fatcat:iec5e4scafcuhg5o4co2vplq4q

Modelling the Structure and Dynamics of Biological Pathways

Laura O'Hara, Alessandra Livigni, Thanos Theo, Benjamin Boyer, Tim Angus, Derek Wright, Sz-Hau Chen, Sobia Raza, Mark W. Barnett, Paul Digard, Lee B. Smith, Tom C. Freeman
2016 PLoS Biology  
We present example pathway models that illustrate of the power of approach to depict a diverse range of systems. Biologists the world over love a good diagram.  ...  The old adage of a picture being worth a thousand words holds true. Diagrams continue to form the bedrock of our efforts to communicate ideas about the complexity of biological systems and pathways.  ...  (D) Pro-apoptotic signalling reaches a peak of approximately 16,000 tokens in interferon-primed macrophages and 14,000 in naïve macrophages, but pro-apoptotic pathways are little activated in the epithelial  ... 
doi:10.1371/journal.pbio.1002530 pmid:27509052 pmcid:PMC4980033 fatcat:5vhifrq5hvez5eaqgmocwnfefa

Differential Signaling Networks Induced by Mild and Lethal Hemorrhagic Fever Virus Infections

G. C. Bowick, S. M. Fennewald, B. L. Elsom, J. F. Aronson, B. A. Luxon, D. G. Gorenstein, N. K. Herzog
2006 Journal of Virology  
Development of new antiviral compounds has been hindered by a lack of understanding of the molecular basis of pathogenesis.  ...  The family Arenaviridae includes several National Institutes of Allergy and Infections Diseases category A select agents which cause hemorrhagic fever.  ...  These studies were supported by grants from DARPA (DAAD19011037), DTRA (DAAD17-01-D0001), and NIH (N01-HV-28184, U01 AI054827, R01 A127744) and by a grant from NIAID to N.K.H. through the Western Regional  ... 
doi:10.1128/jvi.01384-06 pmid:17005702 pmcid:PMC1617297 fatcat:lnmv2z3g5vhyvpexxrlu4uanne

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways

Tom C Freeman, Sobia Raza, Athanasios Theocharidis, Peter Ghazal
2010 BMC Systems Biology  
This work has been driven by the DPM's postgraduate programme in Genomics and Pathway Biology since 2003, where students engage in the curation and notation of biological pathways http://www.pathwaymedicine.ed.ac.uk  ...  ' Framework 6 EC Network of Excellence.  ...  The original Edinburgh Pathway Notation (EPN) scheme [11] was designed to allow the logical depiction of signaling pathways.  ... 
doi:10.1186/1752-0509-4-65 pmid:20478018 pmcid:PMC2878301 fatcat:ol7xnzrrpvb4xofbwf4xl7tz2a

Determining Pharmacological Mechanisms of Chinese Incompatible Herbs Fuzi and Banxia in Chronic Obstructive Pulmonary Disease: A Systems Pharmacology-Based Study

Kaiwen Ni, Xiaolu Cai, Yaling Chen, Linshui Zhou, Ruilin Chen, Suqun Zheng, Zhen Wang, Akhilesh K. Tamrakar
2020 Evidence-Based Complementary and Alternative Medicine  
COPD-related targets were obtained by analyzing the differentially expressed genes between COPD patients and healthy individuals, which were expressed using a Venn diagram of COPD and FB.  ...  Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were conducted. The gene-pathway network was constructed to screen the key target genes.  ...  Acknowledgments e authors would like to thank Editage (http://www. editage.com) for English language editing and biowolf  ... 
doi:10.1155/2020/8365603 pmid:33488748 pmcid:PMC7790578 fatcat:7adobsfgf5cs7fgb2g4jp6r47e

Formal Modeling of the Key Determinants of Hepatitis C Virus (HCV) Induced Adaptive Immune Response Network: An Integrative Approach to Map the Cellular and Cytokine-Mediated Host Immune Regulations [chapter]

Ayesha Obaid, Anam Naz, Shifa Tariq Ashraf, Faryal Mehwish Awan, Aqsa Ikram, Muhammad Tariq Saeed, Abida Raza, Jamil Ahmad, Amjad Ali
2018 Lecture Notes in Computer Science  
Initially, a logic-based diagram is generated based on multiple reported interactions between immune cells and cytokines during host immune response to HCV.  ...  The most probable cycle is predicted based on maximum betweenness centrality. Furthermore, to study the continuous dynamics of the modeled network, a Petri net (PN) model was generated.  ...  To characterize the cytokines mediated HCV clearance and the role of NK 189 cells in the viral clearance, the prior knowledge based logical diagram is reduced to form a BRN. 190 A BRN consists of a set  ... 
doi:10.1007/978-3-319-95171-3_50 fatcat:gxsb7w36jzbgfljqkzgf27vdcy

A digital cmos sequential circuit model for bio-cellular adaptive immune response pathway using phagolysosomic digestion: a digital phagocytosis engine

Sayed Mohammad Rezaul Hasan
2010 Journal of Biomedical Science and Engineering  
The model converts the bio-chemical immune system digestive pathway into a cascade of CMOS multi-step logical transformations from micro-creature ingestion to the secretion of indigestible residuals.  ...  This modeling technique leads to the understanding of cellular immune deficiency diseases of living systems in the form of logical (electrical) faults in a circuit.  ...  Circuit theoretic techniques of modeling this biochemical immune system pathway within a phagocyte compared to other mathematical modeling techniques [7, 8] is the central theme of this paper.  ... 
doi:10.4236/jbise.2010.35065 fatcat:msvdepfrxng6nf5ion6ma6wp2i

Step-wise target controllability identifies dysregulated pathways of macrophage networks in multiple sclerosis [article]

Giulia Bassignana, Jennifer Fransson, Vincent Henry, Olivier Colliot, Violetta Zujovic, Fabrizio De Vico Fallani
2020 arXiv   pre-print
Taking into account these constraints, we propose an optimized heuristic based on the Kalman rank condition to quantify the centrality of a node as the number of target nodes it can control.  ...  We show how the method works for simple network configurations, then we use it to characterize the inflammatory pathways in molecular gene networks associated with macrophage dysfunction in patients with  ...  The research leading to these results has received funding from the French government under management of Agence Nationale de la Recherche as part of the "Investissements d'avenir" program, reference ANR  ... 
arXiv:2003.08913v4 fatcat:hfrkbbr4nnbo5cpzmf2dgjcyu4

A data-driven computational model enables integrative and mechanistic characterization of dynamic macrophage polarization

Chen Zhao, Thalyta X. Medeiros, Richard J. Sové, Brian H. Annex, Aleksander S. Popel
2021 iScience  
, of macrophage polarization driven by a complex multi-pathway signaling network.  ...  Using the model, we generated dynamic phenotype maps in response to numerous combinations of polarizing signals; we also probed into an in silico population of model-based macrophages to examine the impact  ...  TNF activates calcium-nuclear factor of activated T cells (NFAT)c1 signaling pathways in human macrophages. Proc. Natl. Acad. Sci. U S A 108, 1573-1578. Zetterberg, A., and Skold, O. (1969).  ... 
doi:10.1016/j.isci.2021.102112 pmid:33659877 pmcid:PMC7895754 fatcat:7s6pxilrcrajrm4t3xcmh43ywu

The MHC-Based Suppression (MBS) Theory: Implications for Transplantation

Derek W.R. Gray
2008 The Open Transplantation Journal  
This commentary draws attention to a theory that proposes an alternative role for MHC molecules, placing them central to the process of tolerance induction, with major implications for transplantation  ...  Complex areas of scientific endeavor may sometimes benefit from a theoretical and/or reductionist approach to guide the direction of future experiments, perhaps best illustrated by the field of cosmology  ...  Diagram to show the author's suggestion for the molecular pathway for the hypothesised MHC-based suppression signal. D.  ... 
doi:10.2174/1874418400802010040 fatcat:mx4qwc6exvagtht3zlcau4qrcy

The Nuclear Factor NF- B Pathway in Inflammation

T. Lawrence
2009 Cold Spring Harbor Perspectives in Biology  
The nuclear factor NF-kB pathway has long been considered a prototypical proinflammatory signaling pathway, largely based on the role of NF-kB in the expression of proinflammatory genes including cytokines  ...  NF-kB has long been considered the "holy grail" as a target for new anti-inflammatory drugs; however, these recent studies suggest this pathway may prove a difficult target in the treatment of chronic  ...  The nuclear factor NF-kB pathway has long been considered a prototypical proinflammatory signaling pathway, largely based on the role of NF-kB in the expression of proinflammatory genes including cytokines  ... 
doi:10.1101/cshperspect.a001651 pmid:20457564 pmcid:PMC2882124 fatcat:u5uxhu5omfhoxi75ozckkmeg2e
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