메뉴 건너뛰기




Volumn 17, Issue 1, 2016, Pages

A powerful score-based statistical test for group difference in weighted biological networks

Author keywords

Network comparison; Network medicine; Score based statistical test; Systems epidemiology

Indexed keywords

BIOMOLECULES; DISEASES; GENE EXPRESSION; STATISTICAL TESTS;

EID: 84957873113     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-0916-x     Document Type: Article
Times cited : (12)

References (37)
  • 1
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: a network-based approach to human disease
    • Barabasi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011;12(1):56-68.
    • (2011) Nat Rev Genet , vol.12 , Issue.1 , pp. 56-68
    • Barabasi, A.L.1    Gulbahce, N.2    Loscalzo, J.3
  • 3
    • 70249134919 scopus 로고    scopus 로고
    • Molecular networks as sensors and drivers of common human diseases
    • Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009;461(7261):218-23.
    • (2009) Nature , vol.461 , Issue.7261 , pp. 218-223
    • Schadt, E.E.1
  • 4
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004;5(2):101-13.
    • (2004) Nat Rev Genet , vol.5 , Issue.2 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 5
    • 27944493925 scopus 로고    scopus 로고
    • Scale-free networks in cell biology
    • Albert R. Scale-free networks in cell biology. J Cell Sci. 2005;118(Pt 21):4947-57.
    • (2005) J Cell Sci , vol.118 , pp. 4947-4957
    • Albert, R.1
  • 6
    • 43249114206 scopus 로고    scopus 로고
    • Network-based global inference of human disease genes
    • Wu X, Jiang R, Zhang MQ, Li S. Network-based global inference of human disease genes. Mol Syst Biol. 2008;4:189.
    • (2008) Mol Syst Biol , vol.4 , pp. 189
    • Wu, X.1    Jiang, R.2    Zhang, M.Q.3    Li, S.4
  • 7
    • 59849125136 scopus 로고    scopus 로고
    • Dynamic modularity in protein interaction networks predicts breast cancer outcome
    • Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, et al. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol. 2009;27(2):199-204.
    • (2009) Nat Biotechnol , vol.27 , Issue.2 , pp. 199-204
    • Taylor, I.W.1    Linding, R.2    Warde-Farley, D.3    Liu, Y.4    Pesquita, C.5    Faria, D.6
  • 8
    • 84878714179 scopus 로고    scopus 로고
    • Finding the targets of a drug by integration of gene expression data with a protein interaction network
    • Laenen G, Thorrez L, Bornigen D, Moreau Y. Finding the targets of a drug by integration of gene expression data with a protein interaction network. Mol Biosyst. 2013;9(7):1676-85.
    • (2013) Mol Biosyst , vol.9 , Issue.7 , pp. 1676-1685
    • Laenen, G.1    Thorrez, L.2    Bornigen, D.3    Moreau, Y.4
  • 9
    • 84884889100 scopus 로고    scopus 로고
    • Network-based inference framework for identifying cancer genes from gene expression data
    • Yang B, Zhang J, Yin Y, Zhang Y. Network-based inference framework for identifying cancer genes from gene expression data. Biomed Res Int. 2013;2013:401649.
    • (2013) Biomed Res Int , vol.2013 , pp. 401649
    • Yang, B.1    Zhang, J.2    Yin, Y.3    Zhang, Y.4
  • 10
    • 84903142822 scopus 로고    scopus 로고
    • Network based analyses of gene expression profile of LCN2 overexpression in esophageal squamous cell carcinoma
    • Wu B, Li C, Du Z, Yao Q, Wu J, Feng L, et al. Network based analyses of gene expression profile of LCN2 overexpression in esophageal squamous cell carcinoma. Sci Rep. 2014;4:5403.
    • (2014) Sci Rep , vol.4 , pp. 5403
    • Wu, B.1    Li, C.2    Du, Z.3    Yao, Q.4    Wu, J.5    Feng, L.6
  • 11
    • 66749103867 scopus 로고    scopus 로고
    • Opening the Black Box: a motivation for the assessment of mediation
    • Hafeman DM, Schwartz S. Opening the Black Box: a motivation for the assessment of mediation. Int J Epidemiol. 2009;38(3):838-45.
    • (2009) Int J Epidemiol , vol.38 , Issue.3 , pp. 838-845
    • Hafeman, D.M.1    Schwartz, S.2
  • 12
    • 84860724020 scopus 로고    scopus 로고
    • Diving through the "-omics": the case for deep phenotyping and systems epidemiology
    • Haring R, Wallaschofski H. Diving through the "-omics": the case for deep phenotyping and systems epidemiology. OMICS. 2012;16(5):231-4.
    • (2012) OMICS , vol.16 , Issue.5 , pp. 231-234
    • Haring, R.1    Wallaschofski, H.2
  • 14
    • 77953913791 scopus 로고    scopus 로고
    • From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases
    • de la Fuente A. From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases. Trends Genet. 2010;26(7):326-33.
    • (2010) Trends Genet , vol.26 , Issue.7 , pp. 326-333
    • Fuente, A.1
  • 15
    • 84921910280 scopus 로고    scopus 로고
    • Detection for pathway effect contributing to disease in systems epidemiology with a case-control design
    • Ji J, Yuan Z, Zhang X, Li F, Xu J, Liu Y, et al. Detection for pathway effect contributing to disease in systems epidemiology with a case-control design. BMJ Open. 2015;5(1):e006721.
    • (2015) BMJ Open , vol.5 , Issue.1 , pp. e006721
    • Ji, J.1    Yuan, Z.2    Zhang, X.3    Li, F.4    Xu, J.5    Liu, Y.6
  • 16
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: an R package for weighted correlation network analysis
    • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 17
    • 60149089400 scopus 로고    scopus 로고
    • Differential dependency network analysis to identify condition-specific topological changes in biological networks
    • Zhang B, Li H, Riggins RB, Zhan M, Xuan J, Zhang Z, et al. Differential dependency network analysis to identify condition-specific topological changes in biological networks. Bioinformatics. 2009;25(4):526-32.
    • (2009) Bioinformatics , vol.25 , Issue.4 , pp. 526-532
    • Zhang, B.1    Li, H.2    Riggins, R.B.3    Zhan, M.4    Xuan, J.5    Zhang, Z.6
  • 18
    • 80053202843 scopus 로고    scopus 로고
    • A differential network approach to exploring differences between biological states: an application to prediabetes
    • Valcarcel B, Wurtz P, Seicha BNK, Tukiainen T, Kangas AJ, Soininen P, et al. A differential network approach to exploring differences between biological states: an application to prediabetes. PLoS One. 2011;6(9):e24702.
    • (2011) PLoS One , vol.6 , Issue.9 , pp. e24702
    • Valcarcel, B.1    Wurtz, P.2    Seicha, B.N.K.3    Tukiainen, T.4    Kangas, A.J.5    Soininen, P.6
  • 19
    • 84874794126 scopus 로고    scopus 로고
    • An inferential framework for biological network hypothesis tests
    • Yates PD, Mukhopadhyay ND. An inferential framework for biological network hypothesis tests. BMC Bioinformatics. 2013;14:94.
    • (2013) BMC Bioinformatics , vol.14 , pp. 94
    • Yates, P.D.1    Mukhopadhyay, N.D.2
  • 20
    • 33749988857 scopus 로고    scopus 로고
    • Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
    • Reverter A, Ingham A, Lehnert SA, Tan SH, Wang Y, Ratnakumar A, et al. Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer. Bioinformatics. 2006;22(19):2396-404.
    • (2006) Bioinformatics , vol.22 , Issue.19 , pp. 2396-2404
    • Reverter, A.1    Ingham, A.2    Lehnert, S.A.3    Tan, S.H.4    Wang, Y.5    Ratnakumar, A.6
  • 21
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene co-expression network analysis
    • Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4(1):Article17.
    • (2005) Stat Appl Genet Mol Biol , vol.4 , Issue.1
    • Zhang, B.1    Horvath, S.2
  • 22
    • 77950544798 scopus 로고    scopus 로고
    • A statistical framework for differential network analysis from microarray data
    • Gill R, Datta S, Datta S. A statistical framework for differential network analysis from microarray data. BMC Bioinformatics. 2010;11:95.
    • (2010) BMC Bioinformatics , vol.11 , pp. 95
    • Gill, R.1    Datta, S.2    Datta, S.3
  • 23
    • 84907028628 scopus 로고    scopus 로고
    • Comparison of statistical tests for group differences in brain functional networks
    • Kim J, Wozniak JR, Mueller BA, Shen X, Pan W. Comparison of statistical tests for group differences in brain functional networks. Neuroimage. 2014;101:681-94.
    • (2014) Neuroimage , vol.101 , pp. 681-694
    • Kim, J.1    Wozniak, J.R.2    Mueller, B.A.3    Shen, X.4    Pan, W.5
  • 24
    • 0344272718 scopus 로고
    • On the distribution of a linear combination of independent chi squares
    • Fleiss JL. On the distribution of a linear combination of independent chi squares. J Am Stat Assoc. 1971.
    • (1971) J Am Stat Assoc
    • Fleiss, J.L.1
  • 26
    • 52649085237 scopus 로고    scopus 로고
    • Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome
    • Tothill RW, Tinker AV, George J, Brown R, Fox SB, Lade S, et al. Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome. Clin Cancer Res. 2008;14(16):5198-208.
    • (2008) Clin Cancer Res , vol.14 , Issue.16 , pp. 5198-5208
    • Tothill, R.W.1    Tinker, A.V.2    George, J.3    Brown, R.4    Fox, S.B.5    Lade, S.6
  • 28
    • 67651039809 scopus 로고    scopus 로고
    • Notch signaling pathway in ovarian cancer
    • Rose SL. Notch signaling pathway in ovarian cancer. Int J Gynecol Cancer. 2009;19(4):564-6.
    • (2009) Int J Gynecol Cancer , vol.19 , Issue.4 , pp. 564-566
    • Rose, S.L.1
  • 30
    • 84875380606 scopus 로고    scopus 로고
    • DiffCorr: an R package to analyze and visualize differential correlations in biological networks
    • Fukushima A. DiffCorr: an R package to analyze and visualize differential correlations in biological networks. Gene. 2013;518(1):209-14.
    • (2013) Gene , vol.518 , Issue.1 , pp. 209-214
    • Fukushima, A.1
  • 31
    • 84903942924 scopus 로고    scopus 로고
    • OVA66 increases cell growth, invasion and survival via regulation of IGF-1R-MAPK signaling in human cancer cells
    • Rao W, Li H, Song F, Zhang R, Yin Q, Wang Y, et al. OVA66 increases cell growth, invasion and survival via regulation of IGF-1R-MAPK signaling in human cancer cells. Carcinogenesis. 2014;35(7):1573-81.
    • (2014) Carcinogenesis , vol.35 , Issue.7 , pp. 1573-1581
    • Rao, W.1    Li, H.2    Song, F.3    Zhang, R.4    Yin, Q.5    Wang, Y.6
  • 32
    • 84897425195 scopus 로고    scopus 로고
    • Epigenetic silencing of microRNA-199b-5p is associated with acquired chemoresistance via activation of JAG1-Notch1 signaling in ovarian cancer
    • Liu MX, Siu MK, Liu SS, Yam JW, Ngan HY, Chan DW. Epigenetic silencing of microRNA-199b-5p is associated with acquired chemoresistance via activation of JAG1-Notch1 signaling in ovarian cancer. Oncotarget. 2014;5(4):944-58.
    • (2014) Oncotarget , vol.5 , Issue.4 , pp. 944-958
    • Liu, M.X.1    Siu, M.K.2    Liu, S.S.3    Yam, J.W.4    Ngan, H.Y.5    Chan, D.W.6
  • 33
    • 84947025651 scopus 로고    scopus 로고
    • Differentially expressed gene profiles in the serum before and after the ultrasound-guided ethanol sclerotherapy in patients with ovarian endometriomas
    • Wang LL, Cai HQ, Dong XQ, Zhang LW, Jiang SS, Zhao N, et al. Differentially expressed gene profiles in the serum before and after the ultrasound-guided ethanol sclerotherapy in patients with ovarian endometriomas. Clin Biochem. 2015;48(16-17):1131-7.
    • (2015) Clin Biochem , vol.48 , Issue.16-17 , pp. 1131-1137
    • Wang, L.L.1    Cai, H.Q.2    Dong, X.Q.3    Zhang, L.W.4    Jiang, S.S.5    Zhao, N.6
  • 34
    • 84938833420 scopus 로고    scopus 로고
    • NOTCH2 expression is decreased in epithelial ovarian cancer and is related to the tumor histological subtype
    • Galic V, Shawber CJ, Reeves C, Shah M, Murtomaki A, Wright J, et al. NOTCH2 expression is decreased in epithelial ovarian cancer and is related to the tumor histological subtype. Pathol Discov. 2013;1:4.
    • (2013) Pathol Discov , vol.1 , pp. 4
    • Galic, V.1    Shawber, C.J.2    Reeves, C.3    Shah, M.4    Murtomaki, A.5    Wright, J.6
  • 36
    • 79551700835 scopus 로고    scopus 로고
    • ADAM metallopeptidase domain 17 (ADAM17) is naturally processed through major histocompatibility complex (MHC) class I molecules and is a potential immunotherapeutic target in breast, ovarian and prostate cancers
    • Sinnathamby G, Zerfass J, Hafner J, Block P, Nickens Z, Hobeika A, et al. ADAM metallopeptidase domain 17 (ADAM17) is naturally processed through major histocompatibility complex (MHC) class I molecules and is a potential immunotherapeutic target in breast, ovarian and prostate cancers. Clin Exp Immunol. 2011;163(3):324-32.
    • (2011) Clin Exp Immunol , vol.163 , Issue.3 , pp. 324-332
    • Sinnathamby, G.1    Zerfass, J.2    Hafner, J.3    Block, P.4    Nickens, Z.5    Hobeika, A.6
  • 37
    • 25844462410 scopus 로고    scopus 로고
    • A systems biology approach to genetic studies of complex diseases
    • Xiong M, Feghali-Bostwick CA, Arnett FC, Zhou X. A systems biology approach to genetic studies of complex diseases. FEBS Lett. 2005;579(24):5325-32.
    • (2005) FEBS Lett , vol.579 , Issue.24 , pp. 5325-5332
    • Xiong, M.1    Feghali-Bostwick, C.A.2    Arnett, F.C.3    Zhou, X.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.