메뉴 건너뛰기




Volumn 2015, Issue , 2015, Pages

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOPROTEIN; PROTEIN KINASE; TUMOR PROTEIN;

EID: 84943191749     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav020     Document Type: Article
Times cited : (28)

References (50)
  • 1
    • 84891768588 scopus 로고    scopus 로고
    • Protein ontology: A controlled structured network of protein entities
    • Natale, D.A., Arighi, C.N., Blake, J.A. et al. (2013). Protein ontology: A controlled structured network of protein entities. Nucleic Acids Res., 42, D415-D421.
    • (2013) Nucleic Acids Res , vol.42 , pp. D415-D421
    • Natale, D.A.1    Arighi, C.N.2    Blake, J.A.3
  • 8
    • 84869054051 scopus 로고    scopus 로고
    • A travel guide to Cytoscape plugins
    • Saito, R., Smoot, M.E., Ono, K. et al. (2012). A travel guide to Cytoscape plugins. Nat. Methods, 9, 1069-1076.
    • (2012) Nat. Methods , vol.9 , pp. 1069-1076
    • Saito, R.1    Smoot, M.E.2    Ono, K.3
  • 9
    • 80053432627 scopus 로고    scopus 로고
    • Cross-species gene normalization by species inference
    • Wei, C.H. and Kao, H.Y. (2011) Cross-species gene normalization by species inference. BMC Bioinformatics, 3, 1471-2105.
    • (2011) BMC Bioinformatics , vol.3 , pp. 1471-2105
    • Wei, C.H.1    Kao, H.Y.2
  • 10
    • 81455143726 scopus 로고    scopus 로고
    • MinePhos: A literature mining system for protein phosphorylation information extraction
    • Xu, Y., Teng, D. and Lei, Y. (2012) MinePhos: A literature mining system for protein phosphorylation information extraction. IEEE/ACMTrans. Comput. Biol. Bioinform., 9, 311-315.
    • (2012) IEEE/ACMTrans. Comput. Biol. Bioinform , vol.9 , pp. 311-315
    • Xu, Y.1    Teng, D.2    Lei, Y.3
  • 11
    • 84875129833 scopus 로고    scopus 로고
    • Application of text-mining for updating protein post-translational modification annotation in UniProtKB
    • Veuthey, A.L., Bridge, A., Gobeill, J. et al. (2013) Application of text-mining for updating protein post-translational modification annotation in UniProtKB. BMC Bioinformatics, 14, 104.
    • (2013) BMC Bioinformatics , vol.14 , pp. 104
    • Veuthey, A.L.1    Bridge, A.2    Gobeill, J.3
  • 12
    • 33645104154 scopus 로고    scopus 로고
    • Extraction of regulatory gene/protein networks from Medline
    • S?arić, J., Jensen, L.J., Ouzounova, R. et al. (2006). Extraction of regulatory gene/protein networks from Medline. Bioinformatics, 22, 645-650.
    • (2006) Bioinformatics , vol.22 , pp. 645-650
    • Sarić, J.1    Jensen, L.J.2    Ouzounova, R.3
  • 13
    • 84866453775 scopus 로고    scopus 로고
    • Overview of the ID, EPI and REL tasks of BioNLP shared task 2011
    • Pyysalo, S., Ohta, T., Rak, R. et al. (2012) Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics, 13(Suppl. 11), S2.
    • (2012) BMC Bioinformatics , vol.13 , pp. S2
    • Pyysalo, S.1    Ohta, T.2    Rak, R.3
  • 14
    • 84923863282 scopus 로고    scopus 로고
    • Protein-protein interaction predictions using text mining methods
    • Papanikolaou, N., Pavlopoulos, G.A., Theodosiou, T. and Iliopoulos, I. (2015). Protein-protein interaction predictions using text mining methods. Methods, 74, 47-53.
    • (2015) Methods , vol.74 , pp. 47-53
    • Papanikolaou, N.1    Pavlopoulos, G.A.2    Theodosiou, T.3    Iliopoulos, I.4
  • 15
    • 77955465839 scopus 로고    scopus 로고
    • Extracting protein interactions from text with the unified AkaneRE event extraction system
    • Sætre, R., Yoshida, K., Miwa, M. et al. (2010) Extracting protein interactions from text with the unified AkaneRE event extraction system. IEEE/ACM Trans. Comput. Biol. Bioinform., 7, 442-453.
    • (2010) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.7 , pp. 442-453
    • Sætre, R.1    Yoshida, K.2    Miwa, M.3
  • 16
    • 0035755823 scopus 로고    scopus 로고
    • The potential use of SUISEKI as a protein interaction discovery tool
    • Blaschke, C. and Valencia, A. (2001) The potential use of SUISEKI as a protein interaction discovery tool. Genome Inform., 12, 123-134.
    • (2001) Genome Inform , vol.12 , pp. 123-134
    • Blaschke, C.1    Valencia, A.2
  • 17
    • 10244245424 scopus 로고    scopus 로고
    • BioRAT: Extracting biological information from full-length papers
    • Corney, D.P., Buxton, B.F., Langdon, W.B. and Jones, D.T. (2004) BioRAT: Extracting biological information from full-length papers. Bioinformatics, 20, 3206-3213.
    • (2004) Bioinformatics , vol.20 , pp. 3206-3213
    • Corney, D.P.1    Buxton, B.F.2    Langdon, W.B.3    Jones, D.T.4
  • 18
    • 41349107398 scopus 로고    scopus 로고
    • OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
    • Hunter, L., Lu, Z., Firby, J. et al. (2008) OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics, 9, 78.
    • (2008) BMC Bioinformatics , vol.9 , pp. 78
    • Hunter, L.1    Lu, Z.2    Firby, J.3
  • 19
    • 84883377947 scopus 로고    scopus 로고
    • PPIExtractor: A protein interaction extraction and visualization system for biomedical literature
    • Yang, Z., Zhao, Z., Li, Y. et al. (2013). PPIExtractor: A protein interaction extraction and visualization system for biomedical literature. IEEE Trans. Nanobioscience, 12, 173-181.
    • (2013) IEEE Trans. Nanobioscience , vol.12 , pp. 173-181
    • Yang, Z.1    Zhao, Z.2    Li, Y.3
  • 20
    • 77954850017 scopus 로고    scopus 로고
    • PPLook: An automated data mining tool for protein-protein interaction
    • Zhang, S.W., Li, Y.J., Xia, L. and Pan, Q. (2010) PPLook: An automated data mining tool for protein-protein interaction. BMC Bioinformatics, 11, 326.
    • (2010) BMC Bioinformatics , vol.11 , pp. 326
    • Zhang, S.W.1    Li, Y.J.2    Xia, L.3    Pan, Q.4
  • 21
    • 33750589613 scopus 로고    scopus 로고
    • Learning sentence- internal temporal relations
    • Lapata, M. and Lascarides, A. (2006) Learning sentence- internal temporal relations. J. Artif. Intell. Res., 27, 85-117.
    • (2006) J. Artif. Intell. Res , vol.27 , pp. 85-117
    • Lapata, M.1    Lascarides, A.2
  • 24
    • 85011023041 scopus 로고    scopus 로고
    • Causal relation extraction
    • Edited by Calzolari N, Choukri K, Maegaard B, Mariani J, Odjik J, Piperidis S, Tapias D. Marrakech, Morocco: European Language Resources Association (ELRA).
    • Blanco, E., Castell, N. and Moldovan, D. (2008) Causal relation extraction. In: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC'08). Edited by Calzolari N, Choukri K, Maegaard B, Mariani J, Odjik J, Piperidis S, Tapias D. Marrakech, Morocco: European Language Resources Association (ELRA). pp. 310-313.
    • (2008) Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC'08) , pp. 310-313
    • Blanco, E.1    Castell, N.2    Moldovan, D.3
  • 26
    • 77951600909 scopus 로고    scopus 로고
    • Event extraction with complex event classification using rich features
    • Miwa, M., Saetre, R., Kim, J. and Tsujii, J. (2010) Event extraction with complex event classification using rich features. J. Bioinform. Comput. Biol., 8, 131-146.
    • (2010) J. Bioinform. Comput. Biol , vol.8 , pp. 131-146
    • Miwa, M.1    Saetre, R.2    Kim, J.3    Tsujii, J.4
  • 27
    • 84943182930 scopus 로고    scopus 로고
    • Determining causal and non-causal relationships in biomedical text by classifying verbs using a Naive Bayesian Classifier
    • Association for Computational Linguistics, Columbus, OH, USA.
    • van der Horn, P., Bakker, B., Geleijnse, G. et al. (2008) Determining causal and non-causal relationships in biomedical text by classifying verbs using a Naive Bayesian Classifier. In: Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing. Association for Computational Linguistics, Columbus, OH, USA. pp.112-113.
    • (2008) Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing , pp. 112-113
    • Van Der Horn, P.1    Bakker, B.2    Geleijnse, G.3
  • 28
    • 84872188560 scopus 로고    scopus 로고
    • BioCause: Annotating and analysing causality in the biomedical domain
    • Mihəilə, C., Ohta, T., Pyysalo, S. and Ananiadou, S. (2013) BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinformatics, 14, 2.
    • (2013) BMC Bioinformatics , vol.14 , pp. 2
    • Mihəilə, C.1    Ohta, T.2    Pyysalo, S.3    Ananiadou, S.4
  • 29
    • 84855578467 scopus 로고    scopus 로고
    • 2nd edn. Covers Apache Lucene 3.0. Manning Publications, Cherry Hill, NJ
    • McCandless, M., Hatcher, E. and Gospodnetic, O. (2010) Lucene in Action, 2nd edn. Covers Apache Lucene 3.0. Manning Publications, Cherry Hill, NJ.
    • (2010) Lucene in Action
    • McCandless, M.1    Hatcher, E.2    Gospodnetic, O.3
  • 30
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: New features for data integration and network visualization
    • Smoot, M.E., Ono, K., Ruscheinski, J. et al. (2011) Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics, 27, 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3
  • 31
    • 0037032835 scopus 로고    scopus 로고
    • The protein kinase complement of the human genome
    • Manning, G., Whyte, D.B., Martinez, R. et al. (2002) The protein kinase complement of the human genome. Science, 298, 1912-1934.
    • (2002) Science , vol.298 , pp. 1912-1934
    • Manning, G.1    Whyte, D.B.2    Martinez, R.3
  • 32
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
    • (2009) Nat. Protoc , vol.4 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 33
    • 77957140630 scopus 로고    scopus 로고
    • The structural and content aspects of abstracts versus bodies of full text journal articles are different
    • Cohen, K.B., Johnson, H.L., Verspoor, K. et al. (2010) The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics, 11, 492.
    • (2010) BMC Bioinformatics , vol.11 , pp. 492
    • Cohen, K.B.1    Johnson, H.L.2    Verspoor, K.3
  • 34
    • 80455160346 scopus 로고    scopus 로고
    • 14-3-3 proteins as signaling integration points for cell cycle control and apoptosis
    • Gardino, A.K. and Yaffe, M.B. (2011) 14-3-3 proteins as signaling integration points for cell cycle control and apoptosis. Semin. Cell Dev. Biol., 22, 688-695.
    • (2011) Semin. Cell Dev. Biol , vol.22 , pp. 688-695
    • Gardino, A.K.1    Yaffe, M.B.2
  • 35
    • 0030611095 scopus 로고    scopus 로고
    • Mitotic and G2 checkpoint control: Regulation of 14-3-3 protein binding by phosphorylation of Cdc25C on serine-216
    • Peng, C.Y., Graves, P.R., Thoma, R.S. et al. (1997) Mitotic and G2 checkpoint control: Regulation of 14-3-3 protein binding by phosphorylation of Cdc25C on serine-216. Science, 277, 1501-1505.
    • (1997) Science , vol.277 , pp. 1501-1505
    • Peng, C.Y.1    Graves, P.R.2    Thoma, R.S.3
  • 36
    • 0035704094 scopus 로고    scopus 로고
    • 14-3-3 binding regulates catalytic activity of human Wee1 kinase
    • Rothblum-Oviatt, C.J., Ryan, C.E. and Piwnica-Worms, H. (2001) 14-3-3 binding regulates catalytic activity of human Wee1 kinase. Cell Growth Differ., 12, 581-589.
    • (2001) Cell Growth Differ , vol.12 , pp. 581-589
    • Rothblum-Oviatt, C.J.1    Ryan, C.E.2    Piwnica-Worms, H.3
  • 37
    • 33645506912 scopus 로고    scopus 로고
    • Negative cell cycle regulator 14-3-3sigma stabilizes p27 Kip1 by inhibiting the activity of PKB/Akt
    • Yang, H., Zhang, Y., Zhao, R. et al. (2006) Negative cell cycle regulator 14-3-3sigma stabilizes p27 Kip1 by inhibiting the activity of PKB/Akt. Oncogene, 25, 4585-4594.
    • (2006) Oncogene , vol.25 , pp. 4585-4594
    • Yang, H.1    Zhang, Y.2    Zhao, R.3
  • 38
    • 0037047268 scopus 로고    scopus 로고
    • Akt-dependent phosphorylation of p27Kip1 promotes binding to 14-3-3 and cytoplasmic localization
    • Fujita, N., Sato, S., Katayama, K. et al. (2002) Akt-dependent phosphorylation of p27Kip1 promotes binding to 14-3-3 and cytoplasmic localization. J. Biol. Chem., 277, 28706-28713.
    • (2002) J. Biol. Chem , vol.277 , pp. 28706-28713
    • Fujita, N.1    Sato, S.2    Katayama, K.3
  • 39
    • 84872256294 scopus 로고    scopus 로고
    • Deregulated Cdk5 triggers aberrant activation of cell cycle kinases and phosphatases inducing neuronal death
    • Chang, K.H., Vincent, F. and Shah, K. (2012) Deregulated Cdk5 triggers aberrant activation of cell cycle kinases and phosphatases inducing neuronal death. J. Cell. Sci., 125(Pt 21), 5124-5137.
    • (2012) J. Cell. Sci , vol.125 , pp. 5124-5137
    • Chang, K.H.1    Vincent, F.2    Shah, K.3
  • 40
    • 77949912176 scopus 로고    scopus 로고
    • Phosphorylation of PRAS40 on Thr246 by PKB/AKT facilitates efficient phosphorylation of Ser183 by mTORC1
    • Nascimento, E.B., Snel, M., Guigas, B. et al. (2010) Phosphorylation of PRAS40 on Thr246 by PKB/AKT facilitates efficient phosphorylation of Ser183 by mTORC1. Cell Signal., 22, 961-967.
    • (2010) Cell Signal , vol.22 , pp. 961-967
    • Nascimento, E.B.1    Snel, M.2    Guigas, B.3
  • 41
    • 77950872530 scopus 로고    scopus 로고
    • Bioinformatic and experimental survey of 14-3-3-binding sites
    • Johnson, C., Crowther, S., Stafford, M.J. et al. (2010) Bioinformatic and experimental survey of 14-3-3-binding sites. Biochem. J., 427, 69-78.
    • (2010) Biochem. J , vol.427 , pp. 69-78
    • Johnson, C.1    Crowther, S.2    Stafford, M.J.3
  • 42
    • 77956534974 scopus 로고    scopus 로고
    • Nuclear export regulation of COP1 by 14-3-3sigma in response to DNA damage
    • Su, C.H., Zhao, R., Velazquez-Torres, G. et al. (2010) Nuclear export regulation of COP1 by 14-3-3sigma in response to DNA damage. Mol. Cancer, 9, 243.
    • (2010) Mol. Cancer , vol.9 , pp. 243
    • Su, C.H.1    Zhao, R.2    Velazquez-Torres, G.3
  • 43
    • 27844445642 scopus 로고    scopus 로고
    • Perturbations of the AKT signaling pathway in human cancer
    • Altomare, D.A. and Testa, J.R. (2005) Perturbations of the AKT signaling pathway in human cancer. Oncogene, 24, 7455-7464.
    • (2005) Oncogene , vol.24 , pp. 7455-7464
    • Altomare, D.A.1    Testa, J.R.2
  • 44
    • 63749086305 scopus 로고    scopus 로고
    • ErbB receptors and signaling pathways in cancer
    • Hynes, N.E. and MacDonald, G. (2009) ErbB receptors and signaling pathways in cancer. Curr. Opin. Cell Biol., 21, 177-184.
    • (2009) Curr. Opin. Cell Biol , vol.21 , pp. 177-184
    • Hynes, N.E.1    MacDonald, G.2
  • 45
    • 84903701705 scopus 로고    scopus 로고
    • VEGF signaling in cancer treatment
    • Sia, D., Alsinet, C., Newell, P. et al. (2014) VEGF signaling in cancer treatment. Curr. Pharm. Des., 20, 2834-2842.
    • (2014) Curr. Pharm. des , vol.20 , pp. 2834-2842
    • Sia, D.1    Alsinet, C.2    Newell, P.3
  • 46
    • 76249122645 scopus 로고    scopus 로고
    • GLP-1 mediates antiapoptotic effect by phosphorylating Bad through a betaarrestin 1-mediated ERK1/2 activation in pancreatic beta-cells
    • Quoyer, J., Longuet, C., Broca, C. et al. (2010) GLP-1 mediates antiapoptotic effect by phosphorylating Bad through a betaarrestin 1-mediated ERK1/2 activation in pancreatic beta-cells. J. Biol. Chem., 285, 1989-2002.
    • (2010) J. Biol. Chem. , vol.285 , pp. 1989-2002
    • Quoyer, J.1    Longuet, C.2    Broca, C.3
  • 47
    • 0035886878 scopus 로고    scopus 로고
    • Survival-factor-induced phosphorylation of Bad results in its dissociation from Bcl-x(L) but not Bcl-2
    • Hirai, I. and Wang, H.G. (2001) Survival-factor-induced phosphorylation of Bad results in its dissociation from Bcl-x(L) but not Bcl-2. Biochem. J., 359(Pt 2), 345-352.
    • (2001) Biochem. J , vol.359 , pp. 345-352
    • Hirai, I.1    Wang, H.G.2
  • 48
    • 77957141714 scopus 로고    scopus 로고
    • Frequent hyperphosphorylation of AS160 in breast cancer
    • Jiang, X.H., Sun, J.W., Xu, M. et al. (2010) Frequent hyperphosphorylation of AS160 in breast cancer. Cancer Biol. Ther., 10, 362-367.
    • (2010) Cancer Biol. Ther , vol.10 , pp. 362-367
    • Jiang, X.H.1    Sun, J.W.2    Xu, M.3
  • 49
    • 34249738710 scopus 로고    scopus 로고
    • Resistance exercise and insulin regulate AS160 and interaction with 14-3-3 in human skeletal muscle
    • Howlett, K.F., Sakamoto, K., Garnham, A. et al. (2007) Resistance exercise and insulin regulate AS160 and interaction with 14-3-3 in human skeletal muscle. Diabetes, 56, 1608-1614.
    • (2007) Diabetes , vol.56 , pp. 1608-1614
    • Howlett, K.F.1    Sakamoto, K.2    Garnham, A.3
  • 50
    • 78650510609 scopus 로고    scopus 로고
    • MTOR: From growth signal integration to cancer, diabetes and ageing
    • Zoncu, R., Efeyan, A. and Sabatini, D.M. (2011) mTOR: From growth signal integration to cancer, diabetes and ageing. Nat. Rev. Mol. Cell Biol., 12, 21-35.
    • (2011) Nat. Rev. Mol. Cell Biol , vol.12 , pp. 21-35
    • Zoncu, R.1    Efeyan, A.2    Sabatini, D.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.