Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks.
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...
| Publicado en: | Journal of Biomedicine & Biotechnology pp. 13p - 14 |
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| Autores principales: | , , , |
| Formato: | equations & formulas research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
2010
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=105082270&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 105082270 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 11107243 137K jtl: Journal of Biomedicine & Biotechnology issn: 11107243 maglogo: N pubinfo: dt: 2010 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 105082270 105082270 2010748626 NLM20625487 PMC2896678 105082270 ppf: 13p ppct: 1 formats: fmt: @attributes: type: P tig: atl: Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. aug: au: Ozgür A Xiang Z Radev DR He Y affil: Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA. sug: subj: Genes Interferons Vaccines Funding Source Human Immunity Interleukins Protein Kinases Proteins PubMed Tumor Necrosis Factor ab: 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. pubtype: Academic Journal doctype: equations & formulas research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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