Discovering implicit entity relation with the gene-citation-gene network

PloS One
Min SongTamy Chambers

Abstract

In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG) network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG) network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indica...Continue Reading

References

Feb 6, 2004·Proceedings of the National Academy of Sciences of the United States of America·Dennis M Wilkinson, Bernardo A Huberman
May 1, 2004·Nature Genetics·Kevin G BeckerS Alex Wang
Oct 12, 2004·Pharmacogenetics·Jeffrey T Chang, Russ B Altman
Dec 24, 2004·Molecular Biology and Evolution·Matthew W Hahn, Andrew D Kern
Apr 14, 2005·Briefings in Bioinformatics·Aaron M Cohen, William R Hersh
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Jan 19, 2006·Nature Reviews. Genetics·Lars Juhl JensenPeer Bork
May 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kwang-Il GohAlbert-László Barabási
Jul 8, 2008·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Ivana GrbesaKoraljka Gall-Troselj
Jul 18, 2008·Human Molecular Genetics·Isabelle GouletJocelyn Côté
Jul 18, 2008·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Min Jung KimFrank Costantini
Sep 2, 2008·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Andreas HerrlichHarvey Lodish
Jan 21, 2010·Journal of Theoretical Biology·Ernesto Estrada
Mar 30, 2010·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Jing LiXingzhi Xu
May 12, 2011·Nucleic Acids Research·Grace T HuangPanayiotis V Benos
Jun 17, 2011·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Nicholas J BradshawJ Kirsty Millar
Sep 7, 2013·PloS One·Ying DingTamy Chambers

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Software Mentioned

GAD
JAVA
Gephi
MySQL
OMIM
BioGraph
GeneCards
UMLS
PharmGKB

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