Literature-Based Discovery of IFN-γ and Vaccine-Mediated Gene Interaction Networks
Joint Authors
Radev, Dragomir R.
Xiang, Zuoshuang
Özgür, Arzucan
He, Yongqun Oliver
Source
Journal of Biomedicine and Biotechnology
Issue
Vol. 2010, Issue 2010 (31 Dec. 2010), pp.1-13, 13 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2010-06-03
Country of Publication
Egypt
No. of Pages
13
Main Subjects
Abstract EN
Interferon-gamma (IFN-γ) regulates various immune responses that are often critical for vaccine-induced protection.
In order to annotate the IFN-γ-related gene interaction network from a large amount of IFN-γ 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-γ (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-γ relatedness of 56 genes and vaccine development relatedness for 52 genes.
This study also generated many new hypotheses worth further experimental studies.
American Psychological Association (APA)
Özgür, Arzucan& Xiang, Zuoshuang& Radev, Dragomir R.& He, Yongqun Oliver. 2010. Literature-Based Discovery of IFN-γ and Vaccine-Mediated Gene Interaction Networks. Journal of Biomedicine and Biotechnology،Vol. 2010, no. 2010, pp.1-13.
https://search.emarefa.net/detail/BIM-471289
Modern Language Association (MLA)
Özgür, Arzucan…[et al.]. Literature-Based Discovery of IFN-γ and Vaccine-Mediated Gene Interaction Networks. Journal of Biomedicine and Biotechnology No. 2010 (2010), pp.1-13.
https://search.emarefa.net/detail/BIM-471289
American Medical Association (AMA)
Özgür, Arzucan& Xiang, Zuoshuang& Radev, Dragomir R.& He, Yongqun Oliver. Literature-Based Discovery of IFN-γ and Vaccine-Mediated Gene Interaction Networks. Journal of Biomedicine and Biotechnology. 2010. Vol. 2010, no. 2010, pp.1-13.
https://search.emarefa.net/detail/BIM-471289
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-471289