SynthesisJournal of biomedicine & biotechnology2010
Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks.
Synthesis in Journal of biomedicine & biotechnology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 31 citations in OpenAlex.
- Between immunomodulation and immunotolerance: The role of IFNγ in SARS-CoV-2 disease.Cytokine · 2021Review
- A systematic review on literature-based discovery workflow.PeerJ. Computer science · 2019Article
- Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs.Journal of biomedical semantics · 2018Article
- Transcriptomic, Functional, and Network Analyses Reveal Novel Genes Involved in the Interaction BetweenFrontiers in cellular and infection microbiology · 2018Article
- Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.Journal of biomedical semantics · 2017Article
- Integrating text mining, data mining, and network analysis for identifying genetic breast cancer trends.BMC research notes · 2016Article
- Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury.Journal of biomedical semantics · 2015Article
- Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.Journal of biomedical semantics · 2015Article
- Ontology-supported research on vaccine efficacy, safety and integrative biological networks.Expert review of vaccines · 2014Review
- Automating case definitions using literature-based reasoning.Applied clinical informatics · 2013Article
- Computational vaccinology and the ICoVax 2012 workshop.BMC bioinformatics · 2013Article
- Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining.Journal of biomedical semantics · 2012Article
- Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network.BMC immunology · 2011Article
- Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.Journal of biomedical semantics · 2011Article
- Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology.Molecular biotechnology · 2011Article
- BN+1 Bayesian network expansion for identifying molecular pathway elements.Communicative & integrative biology · 2010Article
- Emerging vaccine informatics.Journal of biomedicine & biotechnology · 2010Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Interferon-gamma (IFN-gamma) regulates various immune responses that are often critical for vaccine-induced protection. In order to annotate the IFN-gamma-related gene interaction network from a large amount of IFN-gamma research reported in the literature, a literature-based discovery approach was applied with a combination of natural language processing (NLP) and network centrality analysis. The interaction network of human IFN-gamma (Gene symbol: IFNG) and its vaccine-specific subnetwork were automatically extracted using abstracts from all articles in PubMed. Four network centrality metrics were further calculated to rank the genes in the constructed networks. The resulting generic IFNG network contains 1060 genes and 26313 interactions among these genes. The vaccine-specific subnetwork contains 102 genes and 154 interactions. Fifty six genes such as TNF, NFKB1, IL2, IL6, and MAPK8 were ranked among the top 25 by at least one of the centrality methods in one or both networks. Gene enrichment analysis indicated that these genes were classified in various immune mechanisms such as response to extracellular stimulus, lymphocyte activation, and regulation of apoptosis. Literature evidence was manually curated for the IFN-gamma relatedness of 56 genes and vaccine development relatedness for 52 genes. This study also generated many new hypotheses worth further experimental studies.
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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.