Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks.

Journal of Biomedicine & Biotechnology
Arzucan OzgürYongqun He

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 ...Continue Reading

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Citations

Jun 17, 2011·Briefings in Bioinformatics·Alberto FaroConcetto Spampinato
Jan 1, 2010·Journal of Biomedicine & Biotechnology·Yongqun HeRobert T Chen
Jun 1, 2011·Journal of Biomedical Semantics·Arzucan OzgürYongqun He
Jan 24, 2014·Applied Clinical Informatics·T Botsis, R Ball
Mar 19, 2011·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Spyros N DeftereosAndreas Persidis
Jul 24, 2014·Journal of Receptor and Signal Transduction Research·Akanksha GuptaSonika Bhatnagar
Mar 27, 2013·BMC Bioinformatics·Yongqun HeNikolai Petrovsky
May 21, 2015·Journal of Biomedical Semantics·Michael J CairelliThomas C Rindflesch
Nov 18, 2019·PeerJ. Computer Science·Menasha ThilakaratneThushari Atapattu
Jul 10, 2021·Cytokine·Nataša Todorović-Raković, Jonathan R Whitfield

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Methods Mentioned

BETA
interaction extraction

Software Mentioned

Pathogen - Host Interaction Data Integration and Analysis Syst...
Genia Tagger
MiMI
BioCreative Meta - Server
DAVID
MxTerminator
SVM

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