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Volumn 45, Issue 2, 2017, Pages e8-

A novel method for crosstalk analysis of biological networks: Improving accuracy of pathway annotation

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; ARTIFICIAL NEURAL NETWORK; BENCHMARKING; BINOX ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; DATA PROCESSING; FALSE POSITIVE RESULT; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PROCESS DEVELOPMENT; STATISTICAL ANALYSIS; ALGORITHM; BIOLOGY; GENE REGULATORY NETWORK; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMAN; METABOLISM; PROCEDURES; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 85014051141     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw849     Document Type: Article
Times cited : (30)

References (39)
  • 1
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis: Current approaches and outstanding challenges
    • Khatri,P., Sirota,M. and Butte,A.J. (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol., 8, e1002375.
    • (2012) PLoS Comput. Biol. , vol.8
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3
  • 2
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang,D.W., Sherman,B.T. and Lempicki,R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 4
    • 84891781481 scopus 로고    scopus 로고
    • FunCoup 3.0: Database of genome-wide functional coupling networks
    • Schmitt,T., Ogris,C. and Sonnhammer,E.L.L. (2014) FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res., 42, D380-D388.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D380-D388
    • Schmitt, T.1    Ogris, C.2    Sonnhammer, E.L.L.3
  • 5
    • 65349085291 scopus 로고    scopus 로고
    • Global networks of functional coupling in eukaryotes from comprehensive data integration
    • Alexeyenko,A. and Sonnhammer,E.L.L. (2009) Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res., 19, 1107-1116.
    • (2009) Genome Res. , vol.19 , pp. 1107-1116
    • Alexeyenko, A.1    Sonnhammer, E.L.L.2
  • 7
    • 84908648308 scopus 로고    scopus 로고
    • GeneMANIA: Fast gene network construction and function prediction for Cytoscape
    • Montojo,J., Zuberi,K., Rodriguez,H., Bader,G.D. and Morris,Q. (2014) GeneMANIA: fast gene network construction and function prediction for Cytoscape. F1000Res, 3, 153.
    • (2014) F1000Res , vol.3 , pp. 153
    • Montojo, J.1    Zuberi, K.2    Rodriguez, H.3    Bader, G.D.4    Morris, Q.5
  • 10
    • 84872806763 scopus 로고    scopus 로고
    • Statistical assessment of crosstalk enrichment between gene groups in biological networks
    • McCormack,T., Frings,O., Alexeyenko,A. and Sonnhammer,E.L.L. (2013) Statistical assessment of crosstalk enrichment between gene groups in biological networks. PLoS One, 8, e54945.
    • (2013) PLoS One , vol.8
    • McCormack, T.1    Frings, O.2    Alexeyenko, A.3    Sonnhammer, E.L.L.4
  • 13
    • 0000159985 scopus 로고
    • Importance sampling in the Monte Carlo study of sequential tests
    • Siegmund,D. (1976) Importance sampling in the Monte Carlo study of sequential tests. Ann. Stat., 4, 673-684.
    • (1976) Ann. Stat. , vol.4 , pp. 673-684
    • Siegmund, D.1
  • 14
    • 85014044832 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Stat. Methodol., 57, 289-300.
    • (1995) J. R. Stat. Soc. B Stat. Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 17
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang,D.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, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 19
    • 0021011604 scopus 로고
    • Basal cell carcinomas, gastrointestinal carcinomas, and ulcerative colitis in relation to the disappearance of a plasma factor
    • Klein,A., Storch,B., Meyerson,E., Kadish,U., Kaufmann,H. and Feuerman,E.J. (1982) Basal cell carcinomas, gastrointestinal carcinomas, and ulcerative colitis in relation to the disappearance of a plasma factor. Cancer Detect. Prev., 6, 527-530.
    • (1982) Cancer Detect. Prev. , vol.6 , pp. 527-530
    • Klein, A.1    Storch, B.2    Meyerson, E.3    Kadish, U.4    Kaufmann, H.5    Feuerman, E.J.6
  • 20
    • 55349134911 scopus 로고    scopus 로고
    • Hyaluronan-mediated leukocyte adhesion and dextran sulfate sodium-induced colitis are attenuated in the absence of signal transducer and activator of transcription 1
    • Bandyopadhyay,S.K., Carol,A., Kessler,S.P., Hascall,V.C., Hill,D.R. and Strong,S.A. (2008) Hyaluronan-mediated leukocyte adhesion and dextran sulfate sodium-induced colitis are attenuated in the absence of signal transducer and activator of transcription 1. Am. J. Pathol., 173, 1361-1368.
    • (2008) Am. J. Pathol. , vol.173 , pp. 1361-1368
    • Bandyopadhyay, S.K.1    Carol, A.2    Kessler, S.P.3    Hascall, V.C.4    Hill, D.R.5    Strong, S.A.6
  • 21
    • 84941243860 scopus 로고    scopus 로고
    • Systematic analysis of endometrial cancer-associated hub proteins based on text mining
    • Gao,H. and Zhang,Z. (2015) Systematic analysis of endometrial cancer-associated hub proteins based on text mining. Biomed Res. Int., 2015, 615825.
    • (2015) Biomed Res. Int. , vol.2015
    • Gao, H.1    Zhang, Z.2
  • 22
    • 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
  • 25
    • 0141954162 scopus 로고    scopus 로고
    • Review article: The role of ras superfamily proteins in bladder cancer progression
    • Oxford,G. and Theodorescu,D. (2003) Review article: the role of ras superfamily proteins in bladder cancer progression. J. Urol., 170, 1987-1993.
    • (2003) J. Urol. , vol.170 , pp. 1987-1993
    • Oxford, G.1    Theodorescu, D.2
  • 26
    • 41349107796 scopus 로고    scopus 로고
    • Roles of estrogen receptor α and β in modulating urothelial cell proliferation
    • Teng,J., Wang,Z.-Y., Jarrard,D.F. and Bjorling,D.E. (2008) Roles of estrogen receptor α and β in modulating urothelial cell proliferation. Endocr. Relat. Cancer, 15, 351-364.
    • (2008) Endocr. Relat. Cancer , vol.15 , pp. 351-364
    • Teng, J.1    Wang, Z.-Y.2    Jarrard, D.F.3    Bjorling, D.E.4
  • 27
    • 0034455214 scopus 로고    scopus 로고
    • Efficacy and safety of bacille Calmette-Guerin immunotherapy in superficial bladder cancer
    • Lamm,D.L. (2000) Efficacy and safety of bacille Calmette-Guerin immunotherapy in superficial bladder cancer. Clin. Infect. Dis., 31, S86-S90.
    • (2000) Clin. Infect. Dis. , vol.31 , pp. S86-S90
    • Lamm, D.L.1
  • 32
    • 34748824999 scopus 로고
    • The isolation of intermediary metabolites of l-lysine-U-C14 from tissues of tumor-bearing rats
    • Davis,J.R. and Morris,R.N. (1963) The isolation of intermediary metabolites of l-lysine-U-C14 from tissues of tumor-bearing rats. Cancer Res., 23, 143-147.
    • (1963) Cancer Res. , vol.23 , pp. 143-147
    • Davis, J.R.1    Morris, R.N.2
  • 33
    • 67649239963 scopus 로고    scopus 로고
    • GABA's control of stem and cancer cell proliferation in adult neural and peripheral niches
    • Young,S.Z. and Bordey,A. (2009) GABA's control of stem and cancer cell proliferation in adult neural and peripheral niches. Physiology, 24, 171-185.
    • (2009) Physiology , vol.24 , pp. 171-185
    • Young, S.Z.1    Bordey, A.2
  • 37
    • 0036191219 scopus 로고    scopus 로고
    • A distinctive form of congenital stationary night blindness with cone ON-pathway dysfunction
    • Barnes,C.S., Alexander,K.R. and Fishman,G.A. (2002) A distinctive form of congenital stationary night blindness with cone ON-pathway dysfunction. Ophthalmology, 109, 575-583.
    • (2002) Ophthalmology , vol.109 , pp. 575-583
    • Barnes, C.S.1    Alexander, K.R.2    Fishman, G.A.3
  • 39
    • 85016008675 scopus 로고    scopus 로고
    • PathwAX: A web server for network crosstalk based pathway annotation
    • Ogris,C., Helleday,T. and Sonnhammer,E.L.L. (2016) PathwAX: a web server for network crosstalk based pathway annotation. Nucleic Acids Res., 44, W105-W109.
    • (2016) Nucleic Acids Res. , vol.44 , pp. W105-W109
    • Ogris, C.1    Helleday, T.2    Sonnhammer, E.L.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.