메뉴 건너뛰기




Volumn 7, Issue 6, 2012, Pages

Predicting candidate genes based on combined network topological features: A case study in coronary artery disease

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER ANALYSIS; CORONARY ARTERY DISEASE; ECTFMING METHOD; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; HUMAN; NONHUMAN; PREDICTIVE VALIDITY; PROTEIN PROTEIN INTERACTION; VALIDATION PROCESS;

EID: 84862663073     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039542     Document Type: Article
Times cited : (37)

References (40)
  • 2
    • 33748787676 scopus 로고    scopus 로고
    • Exploring candidate genes for human brain diseases from a brain-specific gene network
    • Liu B, Jiang T, Ma S, Zhao H, Li J, et al. (2006) Exploring candidate genes for human brain diseases from a brain-specific gene network. Biochem Biophys Res Commun 349: 1308-1314.
    • (2006) Biochem Biophys Res Commun , vol.349 , pp. 1308-1314
    • Liu, B.1    Jiang, T.2    Ma, S.3    Zhao, H.4    Li, J.5
  • 3
    • 33747035889 scopus 로고    scopus 로고
    • Predicting disease genes using protein-protein interactions
    • Oti M, Snel B, Huynen MA, Brunner HG, (2006) Predicting disease genes using protein-protein interactions. J Med Genet 43: 691-698.
    • (2006) J Med Genet , vol.43 , pp. 691-698
    • Oti, M.1    Snel, B.2    Huynen, M.A.3    Brunner, H.G.4
  • 4
    • 0035044077 scopus 로고    scopus 로고
    • Assessment of prediction accuracy of protein function from protein-protein interaction data
    • Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T, (2001) Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 18: 523-531.
    • (2001) Yeast , vol.18 , pp. 523-531
    • Hishigaki, H.1    Nakai, K.2    Ono, T.3    Tanigami, A.4    Takagi, T.5
  • 5
    • 33745619564 scopus 로고    scopus 로고
    • Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    • Chua HN, Sung WK, Wong L, (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 22: 1623-1630.
    • (2006) Bioinformatics , vol.22 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.K.2    Wong, L.3
  • 6
    • 43249114206 scopus 로고    scopus 로고
    • Network-based global inference of human disease genes
    • Wu X, Jiang R, Zhang MQ, Li S, (2008) Network-based global inference of human disease genes. Mol Syst Biol 4: 189.
    • (2008) Mol Syst Biol , vol.4 , pp. 189
    • Wu, X.1    Jiang, R.2    Zhang, M.Q.3    Li, S.4
  • 7
    • 58349112341 scopus 로고    scopus 로고
    • Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways
    • Chen L, Zhang L, Zhao Y, Xu L, Shang Y, et al. (2009) Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways. Bioinformatics 25: 237-242.
    • (2009) Bioinformatics , vol.25 , pp. 237-242
    • Chen, L.1    Zhang, L.2    Zhao, Y.3    Xu, L.4    Shang, Y.5
  • 8
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker T, Sharan R, (2008) Protein networks in disease. Genome Res 18: 644-652.
    • (2008) Genome Res , vol.18 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 9
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motif constituents in the yeast protein interaction network
    • Wuchty S, Oltvai ZN, Barabasi AL, (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 35: 176-179.
    • (2003) Nat Genet , vol.35 , pp. 176-179
    • Wuchty, S.1    Oltvai, Z.N.2    Barabasi, A.L.3
  • 10
    • 46249127253 scopus 로고    scopus 로고
    • Identifying gene-disease associations using centrality on a literature mined gene-interaction network
    • Ozgur A, Vu T, Erkan G, Radev DR, (2008) Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics 24: i277-i285.
    • (2008) Bioinformatics , vol.24
    • Ozgur, A.1    Vu, T.2    Erkan, G.3    Radev, D.R.4
  • 11
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V, Mirny LA, (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100: 12123-12128.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 12
    • 0029287487 scopus 로고
    • A measurement-theoretic analysis of the fuzzy logic model of perception
    • Crowther CS, Batchelder WH, Hu X, (1995) A measurement-theoretic analysis of the fuzzy logic model of perception. Psychol Rev 102: 396-408.
    • (1995) Psychol Rev , vol.102 , pp. 396-408
    • Crowther, C.S.1    Batchelder, W.H.2    Hu, X.3
  • 13
    • 17444372787 scopus 로고    scopus 로고
    • Improved prediction of protein-protein binding sites using a support vector machines approach
    • Bradford JR, Westhead DR, (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 21: 1487-1494.
    • (2005) Bioinformatics , vol.21 , pp. 1487-1494
    • Bradford, J.R.1    Westhead, D.R.2
  • 14
    • 0034602774 scopus 로고    scopus 로고
    • Knowledge-based analysis of microarray gene expression data by using support vector machines
    • Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, et al. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 97: 262-267.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 262-267
    • Brown, M.P.1    Grundy, W.N.2    Lin, D.3    Cristianini, N.4    Sugnet, C.W.5
  • 15
    • 0035957531 scopus 로고    scopus 로고
    • A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach
    • Hua S, Sun Z, (2001) A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach. J Mol Biol 308: 397-407.
    • (2001) J Mol Biol , vol.308 , pp. 397-407
    • Hua, S.1    Sun, Z.2
  • 16
    • 0037173010 scopus 로고    scopus 로고
    • Stable expression of calpain 3 from a muscle transgene in vivo: immature muscle in transgenic mice suggests a role for calpain 3 in muscle maturation
    • Spencer MJ, Guyon JR, Sorimachi H, Potts A, Richard I, et al. (2002) Stable expression of calpain 3 from a muscle transgene in vivo: immature muscle in transgenic mice suggests a role for calpain 3 in muscle maturation. Proc Natl Acad Sci U S A 99: 8874-8879.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 8874-8879
    • Spencer, M.J.1    Guyon, J.R.2    Sorimachi, H.3    Potts, A.4    Richard, I.5
  • 17
    • 0345040882 scopus 로고    scopus 로고
    • Support vector machine applications in bioinformatics
    • Byvatov E, Schneider G, (2003) Support vector machine applications in bioinformatics. Appl Bioinformatics 2: 67-77.
    • (2003) Appl Bioinformatics , vol.2 , pp. 67-77
    • Byvatov, E.1    Schneider, G.2
  • 18
    • 33845703344 scopus 로고    scopus 로고
    • What is a support vector machine?
    • Noble WS, (2006) What is a support vector machine? Nat Biotechnol 24: 1565-1567.
    • (2006) Nat Biotechnol , vol.24 , pp. 1565-1567
    • Noble, W.S.1
  • 19
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Kohler S, Bauer S, Horn D, Robinson PN, (2008) Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 82: 949-958.
    • (2008) Am J Hum Genet , vol.82 , pp. 949-958
    • Kohler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 20
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere S, Heymans K, Kuiper M, (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449.
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 21
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5
  • 22
    • 23144464901 scopus 로고    scopus 로고
    • WebGestalt: an integrated system for exploring gene sets in various biological contexts
    • Zhang B, Kirov S, Snoddy J, (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 33: W741-748.
    • (2005) Nucleic Acids Res , vol.33
    • Zhang, B.1    Kirov, S.2    Snoddy, J.3
  • 24
    • 34447136077 scopus 로고    scopus 로고
    • Monocyte cholesterol homeostasis correlates with the presence of detergent resistant membrane microdomains
    • Wolf Z, Orso E, Werner T, Klunemann HH, Schmitz G, (2007) Monocyte cholesterol homeostasis correlates with the presence of detergent resistant membrane microdomains. Cytometry A 71: 486-494.
    • (2007) Cytometry A , vol.71 , pp. 486-494
    • Wolf, Z.1    Orso, E.2    Werner, T.3    Klunemann, H.H.4    Schmitz, G.5
  • 25
    • 0036489731 scopus 로고    scopus 로고
    • Cytokines in coagulation and thrombosis: a preclinical and clinical review
    • Joseph L, Fink LM, Hauer-Jensen M, (2002) Cytokines in coagulation and thrombosis: a preclinical and clinical review. Blood Coagul Fibrinolysis 13: 105-116.
    • (2002) Blood Coagul Fibrinolysis , vol.13 , pp. 105-116
    • Joseph, L.1    Fink, L.M.2    Hauer-Jensen, M.3
  • 26
    • 33744459489 scopus 로고    scopus 로고
    • Risk factor analysis of plasma cytokines in patients with coronary artery disease by a multiplexed fluorescent immunoassay
    • Martins TB, Anderson JL, Muhlestein JB, Horne BD, Carlquist JF, et al. (2006) Risk factor analysis of plasma cytokines in patients with coronary artery disease by a multiplexed fluorescent immunoassay. Am J Clin Pathol 125: 906-913.
    • (2006) Am J Clin Pathol , vol.125 , pp. 906-913
    • Martins, T.B.1    Anderson, J.L.2    Muhlestein, J.B.3    Horne, B.D.4    Carlquist, J.F.5
  • 27
    • 23944513266 scopus 로고    scopus 로고
    • Interferon-gamma and interferon-gamma receptor 1 and 2 gene polymorphisms and restenosis following coronary stenting
    • Tiroch K, von Beckerath N, Koch W, Lengdobler J, Joost A, et al. (2005) Interferon-gamma and interferon-gamma receptor 1 and 2 gene polymorphisms and restenosis following coronary stenting. Atherosclerosis 182: 145-151.
    • (2005) Atherosclerosis , vol.182 , pp. 145-151
    • Tiroch, K.1    von Beckerath, N.2    Koch, W.3    Lengdobler, J.4    Joost, A.5
  • 28
    • 84862655712 scopus 로고    scopus 로고
    • Polymorphisms of the Interferon gamma gene and coronary artery disease in the Korean population
    • Kim HJ, Kang SW, Chung JH, Kim SJ, Choe BK, (2012) Polymorphisms of the Interferon gamma gene and coronary artery disease in the Korean population. Mol Biol Rep 39: 5425-5432.
    • (2012) Mol Biol Rep , vol.39 , pp. 5425-5432
    • Kim, H.J.1    Kang, S.W.2    Chung, J.H.3    Kim, S.J.4    Choe, B.K.5
  • 29
    • 35748983840 scopus 로고    scopus 로고
    • Preproghrelin Leu72Met polymorphism in Chinese subjects with coronary artery disease and controls
    • Tang NP, Wang LS, Yang L, Gu HJ, Zhu HJ, et al. (2008) Preproghrelin Leu72Met polymorphism in Chinese subjects with coronary artery disease and controls. Clin Chim Acta 387: 42-47.
    • (2008) Clin Chim Acta , vol.387 , pp. 42-47
    • Tang, N.P.1    Wang, L.S.2    Yang, L.3    Gu, H.J.4    Zhu, H.J.5
  • 30
    • 25144468784 scopus 로고    scopus 로고
    • Leptin-mediated activation of human platelets: involvement of a leptin receptor and phosphodiesterase 3A-containing cellular signaling complex
    • Elbatarny HS, Maurice DH, (2005) Leptin-mediated activation of human platelets: involvement of a leptin receptor and phosphodiesterase 3A-containing cellular signaling complex. Am J Physiol Endocrinol Metab 289: E695-702.
    • (2005) Am J Physiol Endocrinol Metab , vol.289
    • Elbatarny, H.S.1    Maurice, D.H.2
  • 31
    • 36049041393 scopus 로고    scopus 로고
    • Leptin signalling and leptin-mediated activation of human platelets: importance of JAK2 and the phospholipases Cgamma2 and A2
    • Dellas C, Schafer K, Rohm IK, Lankeit M, Leifheit M, et al. (2007) Leptin signalling and leptin-mediated activation of human platelets: importance of JAK2 and the phospholipases Cgamma2 and A2. Thromb Haemost 98: 1063-1071.
    • (2007) Thromb Haemost , vol.98 , pp. 1063-1071
    • Dellas, C.1    Schafer, K.2    Rohm, I.K.3    Lankeit, M.4    Leifheit, M.5
  • 32
    • 32644456873 scopus 로고    scopus 로고
    • Serum starvation and growth factor receptor expression in vascular smooth muscle cells
    • Zimmermann O, Zwaka TP, Marx N, Torzewski M, Bucher A, et al. (2006) Serum starvation and growth factor receptor expression in vascular smooth muscle cells. J Vasc Res 43: 157-165.
    • (2006) J Vasc Res , vol.43 , pp. 157-165
    • Zimmermann, O.1    Zwaka, T.P.2    Marx, N.3    Torzewski, M.4    Bucher, A.5
  • 33
    • 40649114022 scopus 로고    scopus 로고
    • Low molecular weight hyaluronan increases the Uptaking of oxidized LDL into monocytes
    • Tabata T, Mine S, Okada Y, Tanaka Y, (2007) Low molecular weight hyaluronan increases the Uptaking of oxidized LDL into monocytes. Endocr J 54: 685-693.
    • (2007) Endocr J , vol.54 , pp. 685-693
    • Tabata, T.1    Mine, S.2    Okada, Y.3    Tanaka, Y.4
  • 34
    • 33846120133 scopus 로고    scopus 로고
    • Augmented levels of CD44 in macrophages from atherosclerotic subjects: a possible IL-6-CD44 feedback loop?
    • Hagg D, Sjoberg S, Hulten LM, Fagerberg B, Wiklund O, et al. (2007) Augmented levels of CD44 in macrophages from atherosclerotic subjects: a possible IL-6-CD44 feedback loop? Atherosclerosis 190: 291-297.
    • (2007) Atherosclerosis , vol.190 , pp. 291-297
    • Hagg, D.1    Sjoberg, S.2    Hulten, L.M.3    Fagerberg, B.4    Wiklund, O.5
  • 35
    • 33847420965 scopus 로고    scopus 로고
    • HDL proteomics: pot of gold or Pandora's box?
    • Reilly MP, Tall AR, (2007) HDL proteomics: pot of gold or Pandora's box? J Clin Invest 117: 595-598.
    • (2007) J Clin Invest , vol.117 , pp. 595-598
    • Reilly, M.P.1    Tall, A.R.2
  • 36
    • 35348978183 scopus 로고    scopus 로고
    • Association of plasma levels of F11 receptor/junctional adhesion molecule-A (F11R/JAM-A) with human atherosclerosis
    • Cavusoglu E, Kornecki E, Sobocka MB, Babinska A, Ehrlich YH, et al. (2007) Association of plasma levels of F11 receptor/junctional adhesion molecule-A (F11R/JAM-A) with human atherosclerosis. J Am Coll Cardiol 50: 1768-1776.
    • (2007) J Am Coll Cardiol , vol.50 , pp. 1768-1776
    • Cavusoglu, E.1    Kornecki, E.2    Sobocka, M.B.3    Babinska, A.4    Ehrlich, Y.H.5
  • 37
    • 0025053369 scopus 로고
    • Changes in plasminogen activator inhibitor 1 and tissue-type plasminogen activator during exercise in patients with coronary artery disease
    • Rydzewski A, Sakata K, Kobayashi A, Yamazaki N, Urano T, et al. (1990) Changes in plasminogen activator inhibitor 1 and tissue-type plasminogen activator during exercise in patients with coronary artery disease. Haemostasis 20: 305-312.
    • (1990) Haemostasis , vol.20 , pp. 305-312
    • Rydzewski, A.1    Sakata, K.2    Kobayashi, A.3    Yamazaki, N.4    Urano, T.5
  • 38
    • 0026676001 scopus 로고
    • Thrombolysis with recombinant human tissue-type plasminogen activator during instability in coronary artery disease: effect on myocardial ischemia and need for coronary revascularization. TRIC Study Group
    • Karlsson JE, Berglund U, Bjorkholm A, Ohlsson J, Swahn E, et al. (1992) Thrombolysis with recombinant human tissue-type plasminogen activator during instability in coronary artery disease: effect on myocardial ischemia and need for coronary revascularization. TRIC Study Group. Am Heart J 124: 1419-1426.
    • (1992) Am Heart J , vol.124 , pp. 1419-1426
    • Karlsson, J.E.1    Berglund, U.2    Bjorkholm, A.3    Ohlsson, J.4    Swahn, E.5
  • 39
    • 33646884801 scopus 로고    scopus 로고
    • Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
    • Franke L, van Bakel H, Fokkens L, de Jong ED, Egmont-Petersen M, et al. (2006) Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet 78: 1011-1025.
    • (2006) Am J Hum Genet , vol.78 , pp. 1011-1025
    • Franke, L.1    van Bakel, H.2    Fokkens, L.3    de Jong, E.D.4    Egmont-Petersen, M.5
  • 40


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.