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

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Song, Min ^a   Han, Nam Gi ^a   Kim, Yong Hwan ^a   Ding, Ying ^b   Chambers, Tamy ^b  

^a Yonsei University   (South Korea)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATR PROTEIN; CELL CYCLE PROTEIN 20; CHECKPOINT KINASE 2; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; OCTAMER TRANSCRIPTION FACTOR 4; PROTEIN BCL 2; PROTEIN MDM2; RAD51 PROTEIN; RAD52 PROTEIN; TRANSCRIPTION FACTOR CLOCK; TRANSCRIPTION FACTOR E2F1; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2;

ARTICLE; ATR GENE; BCL2 GENE; BUB1B GENE; CDKN2A GENE; CHEK2 GENE; CLOCK GENE; DMC1 GENE; DNMT3B GENE; E2F1 GENE; GENE CITATION GENE NETWORK; GENE CLUSTER; GENE IDENTIFICATION; GENE INTERACTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC MODEL; GENETIC PROCEDURES; INTERMETHOD COMPARISON; MDM2 GENE; MXI1 GENE; NANOG GENE; ONCOGENE H RAS; ONCOGENE MYC; PARK2 GENE; PINK1 GENE; POU5F1 GENE; RAD51 GENE; RAD52 GENE; SOX2 GENE; TP63 GENE; TP73 GENE; TUMOR SUPPRESSOR GENE; VALIDATION PROCESS;

COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; GENE REGULATORY NETWORKS; HUMANS; PROTEIN INTERACTION MAPPING;

EID: 84892918492     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084639     Document Type: Article

References (42)

1. Galvez C (2008) Knowledge Management for Biomedical Literature: The Function of Text-Mining Technologies in Life-Science Research. Conference Preceedings of the International Technology. Education and Development Conference, Valencia, Spain.
2. Ding Y, Song M, Han J, Yu Q, Yan E et al. (2013) Entitymetrics: Measuring the impact of entities. PLOS ONE.
3. Song M, Kim S, Zhang G, Ding Y, Chambers T. Productivity and influence in bioinformatics: A biliographic analysis using PubMed central. Journal of American Society for Information Science and Technology.
4. Goh KI, Cusick ME, Valle D, Childs B, Vidal M et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690. doi: 10.1073/pnas.0701361104. PubMed: 17502601.
5. Stapley BJ, Benoit G (2000) Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pacific Symposium on Biocomputing 5: 526-537. PubMed: 10902200.
6. Jensen LJ, Saric J, Bork P (2006) Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 7: 119-129. doi:10.1038/nrg1768. PubMed: 16418747.
7. Stephens M, Palakal M, Mukhopadhyay S, Raje R (2001) Detecting gene relations from Medline abstracts. Pacific Symposium On Biocomputing 6: 483-496. PubMed: 11262966.
8. Wren JD, Garner HR (2004) Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics 20: 191-198. doi:10.1093/bioinformatics/btg390. PubMed: 14734310.
9. Chang JT, Altman RB (2004) Extracting and characterizing gene-drug relationships from the literature. Pharmacogenetics and Genomics 14: 577-586. PubMed: 15475731.
10. Wilkinson DM, Huberman BA (2004) A method for finding communities of related genes. Proceedings of the National Academy of Sciences of the United States of America 6: 5241-5248.
11. Özgür A, Vu T, Erkan G, Radev DR (2008) Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics 24: 277-285. doi:10.1093/ bioinformatics/btn182. PubMed: 18586725.
12. Cohen AM, Hersh WR (2005) A survey of current work in biomedical text mining. Brief Bioinform 6: 57-71. doi:10.1093/bib/6.1.57. PubMed: 15826357.
13. Cooper JW, Kershenbaum A (2005) Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information. BMC Bioinformatics 6. PubMed: 15941473.
14. Li S, Wu L, Zhang Z (2006) Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 22: 2143-2150. doi:10.1093/bioinformatics/btl363. PubMed: 16820422.
15. Li X, Chen H, Huang Z, Su H, Martinez JD (2007) Global mapping of gene/protein interactions in PubMed abstracts: A framework and an experiment with P53 interactions. J Biomed Inform 40: 453-464. doi: 10.1016/j.jbi.2007.01. 001. PubMed: 17317333.
16. Patel M, Bullinaria JA, Levy JP (1997) Extracting Semantic Representations from Large Text Corpora. 4th Neural Computation and Psychology Workshop, London, 9-11. pp. 199-212.
17. Huang GT, Athanassiou C, Benos PV (2011) mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res 39: W416-W423. doi:10.1093/nar/gkr276. PubMed: 21558324.
18. McCallum A, Li W (2003) Early results for named entity recognition with conditional random fields, feature induction and web-enhanced lexicons. Proceedings of the seventh conference on Natural language learning at HLT-NAACL-2003 - Volume 4. 4: 188-191.
19. Bastian M, Heymann S, Jacomy M. (2009) Gephi: an open source software for exploring and manipulating networks. Proceedings of the 3rd Int'l AAAI Conference on Weblogs and Social Media, San Jose, CA, May 17-20. pp. 361-362.
20. Estrada E (2010) Generalized walks-based centrality measures for complex biological networks. J Theor Biol 263(4): 556-565. doi: 10.1016/j.jtbi.2010.01. 014. PubMed: 20085771.
21. Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22: 803-806. doi:10.1093/molbev/msi072. PubMed: 15616139.
22. Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: 535-539. doi:10.1093/nar/gkj109. PubMed: 16381927.
23. Becker KG, Barnes KC, Bright TJ, Wang SA (2004) The genetic association database. Nat Genet 36: 431-432. doi:10.1038/ng0504-431. PubMed: 15118671.
24. Brandes U (2001) A faster algorithm for betweenness centrality. Journal of Mathematical Sociology 25: 162-177.
25. Blondel VD, Guillaume J-L, Lambiotte R, Lefebvre E (2008). Fast Unfolding of Communities in Large Networks. arXiv: 0803.0476
26. Lodish H, Berk A, Matsudaira P, Kaiser CA, Scott MP et al. (2008). Molecular Cell Biology.
27. Zhao L, Rosales C, Seburn K, Ron D, Ackerman SL (2010) Alteration of the unfolded protein response modifies neurodegeneration in a mouse model of Marinesco-Sjögren syndrome. Hum Mol Genet 19(1): 25-35. doi:10.1093/hmg/ddp464. PubMed: 19801575.
28. Goulet I, Boisvenue S, Mokas S, Mazroui R, Côté J (2008) TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. Hum Mol Genet 17(19): 3055-3074. doi:10.1093/hmg/ddn203. PubMed: 18632687.
29. Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A et al. (2004) A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat Genet 36(7): 714-719. doi: 10.1038/ng1387. PubMed: 15220921.
30. Haÿ E, Laplantine E, Geoffroy V, Frain M, Kohler T et al. (2009) N-cadherin interacts with axin and LRP5 to negatively regulate Wnt/betacatenin signaling, osteoblast function, and bone formation. N-cadherin interacts with axin and LRP5 to negatively regulate Wnt/beta-catenin signaling, osteoblast function, and bone formation. Mol Cell Biol 29(4): 953-964. doi:10.1128/MCB. 00349-08. PubMed: 19075000.
31. Mao J, Wang J, Liu B, Pan W, Farr GH 3rd et al. (2001) Low-density lipoprotein receptor-related protein-5 binds to Axin and regulates the canonical Wnt signaling pathway. Mol Cell 7(4): 801-809. doi:10.1016/S1097-2765(01)00224- 6. PubMed: 11336703.
32. Ding Y, Xi Y, Chen T, Wang JY, Tao DL et al. (Sep 82008) Caprin-2 enhances canonical Wnt signaling through regulating LRP5/6 phosphorylation. J Cell Biol Sep 8;182(5): 865-872. doi:10.1083/jcb. 200803147. PubMed: 18762581.
33. Kim MJ, Chia IV, Costantini F (Nov2008) SUMOylation target sites at the C terminus protect Axin from ubiquitination and confer protein stability. FASEB J 22(11): 3785-3794. doi:10.1096/fj.08-113910. PubMed: 18632848.
34. Grbesa I, Marinkovic M, Ivkic M, Kruslin B, Novak-Kujundzic R et al. (2008) Loss of imprinting of IGF2 and H19, loss of heterozygosity of IGF2R and CTCF, and Helicobacter pylori infection in laryngeal squamous cell carcinoma. Journal of Molecular Medicine 86: 1057-1066. doi:10.1007/s00109-008-0369-4. PubMed: 18604514.
35. Tost J, Jammes H, Dupont J-M, Buffat C, Robert B et al. (2006) Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region. Nucleic Acids Res 34: 5438-5448. doi:10.1093/nar/gkl657. PubMed: 17012269.
36. De Castro Valente Esteves LI, De Karla Cervigne N, Do Carmo Javaroni A, Magrin J, Kowalski LP et al. (2006) H19-DMR allele-specific methylation analysis reveals epigenetic heterogeneity of CTCF binding site 6 but not of site 5 in head-and-neck carcinomas: A pilot case-control analysis. Int J Mol Med 17: 397-404. PubMed: 16391843. Available online at: PubMed: 16391843
37. Bradshaw NJ, Soares DC, Carlyle BC, Ogawa F, Davidson-Smith H et al. (2011) PKA Phosphorylation of NDE1 Is DISC1/PDE4 Dependent and Modulates Its Interaction with LIS1 and NDEL1. J Neurosci 31: 9043-9054. doi:10.1523/ JNEUROSCI.5410-10.2011. PubMed: 21677187.
38. Moens LN, De Rijk P, Reumers J, Maarten JA, Bossche VD et al. (2011) Sequencing of DISC1 Pathway Genes Reveals Increased Burden of Rare Missense Variants in Schizophrenia Patients from a Northern Swedish Population. PLOS ONE 6.
39. Burdick KE, Kamiya A, Hodgkinson CA, Lencz T, DeRosse P et al. (2008) Elucidating the relationship between DISC1, NDEL1 and NDE1 and the risk for schizophrenia: Evidence of epistasis and competitive binding. Hum Mol Genet 17: 2462-2473. doi:10.1093/hmg/ddn146. PubMed: 18469341.
40. Li J, Wang J, Jiao H, Liao J, Xu X (2010) Cytokinesis and cancer: Polo loves ROCK"n" Rho(A). J Genet Genomics 37: 159-172. doi:10.1016/S1673-8527(09)60034-5. PubMed: 20347825.
41. Wolfe BA, Takaki T, Petronczki M, Glotzer M (2009) Polo-Like Kinase 1 Directs Assembly of the HsCyk-4 RhoGAP/Ect2 RhoGEF Complex to Initiate Cleavage Furrow Formation. PLoS Biol 7: e1000110. PubMed: 19468300.
42. Niiya F, Tatsumoto T, Lee KS, Miki T (2006) Phosphorylation of the cytokinesis regulator ECT2 at G2/M phase stimulates association of the mitotic kinase Plk1 and accumulation of GTP-bound RhoA. Oncogene 25: 827-837. doi:10.1038/sj.onc.1209124. PubMed: 16247472.