ArticlePloS one2011
Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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.
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Who cites it
23 citing papers in PubMed, 36 citations in OpenAlex.
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- Full Spectrum of LPS Activation in Alveolar Macrophages of Healthy Volunteers by Whole Transcriptomic Profiling.PloS one · 2016Article
- Proteomic Analysis Reveals Distinct Metabolic Differences Between Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF) and Macrophage Colony Stimulating Factor (M-CSF) Grown Macrophages Derived from Murine Bone Marrow Cells.Molecular & cellular proteomics : MCP · 2015Article
- RNA-sequencing reveals transcriptional up-regulation of Trem2 in response to bexarotene treatment.Neurobiology of disease · 2015Article
- Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.Nucleic acids research · 2015Article
- Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.Cell reports · 2015Article
- Transcriptome-based network analysis reveals a spectrum model of human macrophage activation.Immunity · 2014Article
- Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis.Frontiers in immunology · 2014Article
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- A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses.PloS one · 2013Article
- Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.Current topics in microbiology and immunology · 2013Review
- Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data.Expert opinion on medical diagnostics · 2013Article
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- Characterization of the microRNAome in porcine reproductive and respiratory syndrome virus infected macrophages.PloS one · 2013Article
- Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis.BMC systems biology · 2012Article
- Differences in gene expression and cytokine production by crystalline vs. amorphous silica in human lung epithelial cells.Particle and fibre toxicology · 2012Article
- Modeling dynamic regulatory processes in stroke.PLoS computational biology · 2012Article
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Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
We have investigated macrophage activation using computational analyses of a compendium of transcriptomic data covering responses to agonists of the TLR pathway, Salmonella infection, and manufactured amorphous silica nanoparticle exposure. We inferred regulatory relationship networks using this compendium and discovered that genes with high betweenness centrality, so-called bottlenecks, code for proteins targeted by pathogens. Furthermore, combining a novel set of bioinformatics tools, topological analysis with analysis of differentially expressed genes under the different stimuli, we identified a conserved core response module that is differentially expressed in response to all studied conditions. This module occupies a highly central position in the inferred network and is also enriched in genes preferentially targeted by pathogens. The module includes cytokines, interferon induced genes such as Ifit1 and 2, effectors of inflammation, Cox1 and Oas1 and Oasl2, and transcription factors including AP1, Egr1 and 2 and Mafb. Predictive modeling using a reverse-engineering approach reveals dynamic differences between the responses to each stimulus and predicts the regulatory influences directing this module. We speculate that this module may be an early checkpoint for progression to apoptosis and/or inflammation during macrophage activation.
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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.