ArticleBMC systems biology2010
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems.
Article in BMC systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed.
- Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease.Database : the journal of biological databases and curation · 2021Article
- Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies.BMC research notes · 2018Article
- A graphical and computational modeling platform for biological pathways.Nature protocols · 2018Article
- Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Cardiac Fibroblast Activation Post-Myocardial Infarction: Current Knowledge Gaps.Trends in pharmacological sciences · 2017Review
- Knowledge gaps to understanding cardiac macrophage polarization following myocardial infarction.Biochimica et biophysica acta · 2016Review
- Modelling the Structure and Dynamics of Biological Pathways.PLoS biology · 2016Article
- The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms.BMC systems biology · 2015Article
- A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages.Genes & development · 2015Article
- Visualisation of BioPAX Networks using BioLayout Express (3D).F1000Research · 2014Article
- QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells.Bioinformatics (Oxford, England) · 2013Article
- Structural and functional annotation of the porcine immunome.BMC genomics · 2013Article
- Mining large-scale response networks reveals 'topmost activities' in Mycobacterium tuberculosis infection.Scientific reports · 2013Article
- Systems biology of host-fungus interactions: turning complexity into simplicity.Current opinion in microbiology · 2012Review
- Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.BMC systems biology · 2012Article
- Article
- Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation.PloS one · 2011Article
- The in silico macrophage: toward a better understanding of inflammatory disease.Genome medicine · 2011Article
- DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.Immunome research · 2010Article
- Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase.BMC systems biology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
backgroundIn an effort to better understand the molecular networks that underpin macrophage activation we have been assembling a map of relevant pathways. Manual curation of the published literature was carried out in order to define the components of these pathways and the interactions between them. This information has been assembled into a large integrated directional network and represented graphically using the modified Edinburgh Pathway Notation (mEPN) scheme.
resultsThe diagram includes detailed views of the toll-like receptor (TLR) pathways, other pathogen recognition systems, NF-kappa-B, apoptosis, interferon signalling, MAP-kinase cascades, MHC antigen presentation and proteasome assembly, as well as selected views of the transcriptional networks they regulate. The integrated pathway includes a total of 496 unique proteins, the complexes formed between them and the processes in which they are involved. This produces a network of 2,170 nodes connected by 2,553 edges.
conclusionsThe pathway diagram is a navigable visual aid for displaying a consensus view of the pathway information available for these systems. It is also a valuable resource for computational modelling and aid in the interpretation of functional genomics data. We envisage that this work will be of value to those interested in macrophage biology and also contribute to the ongoing Systems Biology community effort to develop a standard notation scheme for the graphical representation of biological pathways.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.