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Volumn 12, Issue 4, 2014, Pages

Identification of inflammatory bowel disease-related proteins using a reverse k-nearest neighbor search

Author keywords

disease related protein; Inflammatory bowel disease; protein protein interaction network; reverse k nearest neighbor search

Indexed keywords

INTERLEUKIN RECEPTOR; INTERLEUKIN-20 RECEPTOR; JAK2 PROTEIN, HUMAN; JANUS KINASE 2; PROTEIN;

EID: 84906717523     PISSN: 02197200     EISSN: 17576334     Source Type: Journal    
DOI: 10.1142/S0219720014500176     Document Type: Article
Times cited : (14)

References (75)
  • 3
    • 34547176642 scopus 로고    scopus 로고
    • Unravelling the pathogenesis of inflammatory bowel disease
    • Xavier RJ, Podolsky DK, Unravelling the pathogenesis of inflammatory bowel disease, Nature 448:427-434, 2007.
    • (2007) Nature , vol.448 , pp. 427-434
    • Xavier, R.J.1    Podolsky, D.K.2
  • 4
    • 79955677184 scopus 로고    scopus 로고
    • Current therapeutic approaches in inflammatory bowel disease
    • Sohrabpour AA, Malekzadeh R, Keshavarzian A, Current therapeutic approaches in inflammatory bowel disease, Curr Pharm Des 16:3668-3683, 2010.
    • (2010) Curr Pharm des , vol.16 , pp. 3668-3683
    • Sohrabpour, A.A.1    Malekzadeh, R.2    Keshavarzian, A.3
  • 5
    • 0242384062 scopus 로고    scopus 로고
    • Surgery for inflammatory bowel diseases
    • McLeod RS, Surgery for inflammatory bowel diseases, Dig Dis 21:168-179, 2003.
    • (2003) Dig Dis , vol.21 , pp. 168-179
    • McLeod, R.S.1
  • 6
    • 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 12:56-68, 2011.
    • (2011) Nat Rev Genet , vol.12 , pp. 56-68
    • Barabasi, A.L.1    Gulbahce, N.2    Loscalzo, J.3
  • 9
    • 79958795334 scopus 로고    scopus 로고
    • Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases
    • Bauer-Mehren A, Bundschus M, Rautschka M, Mayer MA, Sanz F, Furlong LI, Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases, PLoS One 6:e20284, 2011.
    • (2011) PLoS One , vol.6
    • Bauer-Mehren, A.1    Bundschus, M.2    Rautschka, M.3    Mayer, M.A.4    Sanz, F.5    Furlong, L.I.6
  • 10
    • 66749185818 scopus 로고    scopus 로고
    • Progress in genome-wide association studies of human height
    • Hirschhorn JN, Lettre G, Progress in genome-wide association studies of human height, Horm Res 71 Suppl 2:5-13, 2009.
    • (2009) Horm Res , vol.71 , Issue.SUPPL. 2 , pp. 5-13
    • Hirschhorn, J.N.1    Lettre, G.2
  • 11
    • 58149333555 scopus 로고    scopus 로고
    • Autoimmune diseases: Insights from genome-wide association studies
    • Lettre G, Rioux JD, Autoimmune diseases: Insights from genome-wide association studies, Hum Mol Genet 17:R116-121, 2008.
    • (2008) Hum Mol Genet , vol.17
    • Lettre, G.1    Rioux, J.D.2
  • 13
    • 33746631391 scopus 로고    scopus 로고
    • Evolutionary and physiological importance of hub proteins
    • Batada NN, Hurst LD, Tyers M, Evolutionary and physiological importance of hub proteins, PLoS Comput Biol2:e88, 2006.
    • (2006) PLoS Comput Biol , vol.2
    • Batada, N.N.1    Hurst, L.D.2    Tyers, M.3
  • 14
    • 31344478575 scopus 로고    scopus 로고
    • Virtual identification of essential proteins within the protein interaction network of yeast
    • Estrada E, Virtual identification of essential proteins within the protein interaction network of yeast, Proteomics 6:35-40, 2006.
    • (2006) Proteomics , vol.6 , pp. 35-40
    • Estrada, E.1
  • 16
    • 33748706765 scopus 로고    scopus 로고
    • Global topological features of cancer proteins in the human interactome
    • Jonsson PF, Bates PA, Global topological features of cancer proteins in the human interactome, Bioinformatics 22:2291-2297, 2006.
    • (2006) Bioinformatics , vol.22 , pp. 2291-2297
    • Jonsson, P.F.1    Bates, P.A.2
  • 17
    • 48449102450 scopus 로고    scopus 로고
    • Hubba: Hub objects analyzer - A framework of interactome hubs identification for network biology
    • Lin CY, Chin CH, Wu HH, Chen SH, Ho CW, Ko MT, Hubba: Hub objects analyzer - a framework of interactome hubs identification for network biology, Nucleic Acids Res 36:W438-443, 2008.
    • (2008) Nucleic Acids Res , vol.36
    • Lin, C.Y.1    Chin, C.H.2    Wu, H.H.3    Chen, S.H.4    Ho, C.W.5    Ko, M.T.6
  • 18
    • 77955077532 scopus 로고    scopus 로고
    • Identifying essential genes in bacterial metabolic networks with machine learning methods
    • Plaimas K, Eils R, Konig R, Identifying essential genes in bacterial metabolic networks with machine learning methods, BMC Syst Biol 4:56, 2010.
    • (2010) BMC Syst Biol , vol.4 , pp. 56
    • Plaimas, K.1    Eils, R.2    Konig, R.3
  • 19
    • 33751017706 scopus 로고    scopus 로고
    • Discovering disease-genes by topological features in human protein-protein interaction network
    • Xu J, Li Y, Discovering disease-genes by topological features in human protein-protein interaction network, Bioinformatics 22:2800-2805, 2006.
    • (2006) Bioinformatics , vol.22 , pp. 2800-2805
    • Xu, J.1    Li, Y.2
  • 20
    • 84872187316 scopus 로고    scopus 로고
    • Disentangling function from topology to infer the network properties of disease genes
    • Ghersi D, Singh M, Disentangling function from topology to infer the network properties of disease genes, BMC Syst Biol 7:5, 2013.
    • (2013) BMC Syst Biol , vol.7 , pp. 5
    • Ghersi, D.1    Singh, M.2
  • 21
    • 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, Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions, Bioinformatics 22:1623-1630, 2006.
    • (2006) Bioinformatics , vol.22 , pp. 1623-1630
    • Chua, H.N.1    Sung, W.K.2    Wong, L.3
  • 22
    • 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, Assessment of prediction accuracy of protein function from protein-protein interaction data, Yeast 18:523-531, 2001.
    • (2001) Yeast , vol.18 , pp. 523-531
    • Hishigaki, H.1    Nakai, K.2    Ono, T.3    Tanigami, A.4    Takagi, T.5
  • 24
    • 33845545435 scopus 로고    scopus 로고
    • The modular nature of genetic diseases
    • Oti M, Brunner HG, The modular nature of genetic diseases, Clin Genet 71:1-11, 2007.
    • (2007) Clin Genet , vol.71 , pp. 1-11
    • Oti, M.1    Brunner, H.G.2
  • 25
    • 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 4:189, 2008.
    • (2008) Mol Syst Biol , vol.4 , pp. 189
    • Wu, X.1    Jiang, R.2    Zhang, M.Q.3    Li, S.4
  • 26
    • 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, Wang Q, Li W, Wang H, Li X, Prioritizing risk pathways: A novel association approach to searching for disease pathways fusing SNPs and pathways, Bioinformatics 25:237-242, 2009.
    • (2009) Bioinformatics , vol.25 , pp. 237-242
    • Chen, L.1    Zhang, L.2    Zhao, Y.3    Xu, L.4    Shang, Y.5    Wang, Q.6    Li, W.7    Wang, H.8    Li, X.9
  • 30
    • 77957726465 scopus 로고    scopus 로고
    • Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology
    • Ning K, Ng HK, Srihari S, Leong HW, Nesvizhskii AI, Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology, BMC Bioinformatics 11:505, 2010.
    • (2010) BMC Bioinformatics , vol.11 , pp. 505
    • Ning, K.1    Ng, H.K.2    Srihari, S.3    Leong, H.W.4    Nesvizhskii, A.I.5
  • 33
    • 0039845446 scopus 로고    scopus 로고
    • Influence sets based on reverse nearest neighbor queries
    • Korn F, Muthukrishnan S, Influence sets based on reverse nearest neighbor queries, SIGMOD Rec 29:201-212, 2000.
    • (2000) SIGMOD Rec , vol.29 , pp. 201-212
    • Korn, F.1    Muthukrishnan, S.2
  • 37
    • 84883697796 scopus 로고    scopus 로고
    • CC Chemokine ligand 20 and its cognate receptor CCR6 in mucosal T cell immunology and inflammatory bowel disease: Odd couple or axis of evil?
    • Lee AY, Eri R, Lyons AB, Grimm MC, Korner H, CC Chemokine ligand 20 and its cognate receptor CCR6 in mucosal T cell immunology and inflammatory bowel disease: Odd couple or axis of evil?, Front Immunol 4:194, 2013.
    • (2013) Front Immunol , vol.4 , pp. 194
    • Lee, A.Y.1    Eri, R.2    Lyons, A.B.3    Grimm, M.C.4    Korner, H.5
  • 38
    • 0035988250 scopus 로고    scopus 로고
    • The conversion of redox status of peritoneal macrophages during pathological progression of spontaneous inflammatory bowel disease in Janus family tyrosine kinase 3(-/-) and IL-2 receptor gamma(-/-) mice
    • Murata Y, Yamashita A, Saito T, Sugamura K, Hamuro J, The conversion of redox status of peritoneal macrophages during pathological progression of spontaneous inflammatory bowel disease in Janus family tyrosine kinase 3(-/-) and IL-2 receptor gamma(-/-) mice, Int Immunol 14:627-636, 2002.
    • (2002) Int Immunol , vol.14 , pp. 627-636
    • Murata, Y.1    Yamashita, A.2    Saito, T.3    Sugamura, K.4    Hamuro, J.5
  • 40
    • 84893676516 scopus 로고    scopus 로고
    • Indicaxanthin inhibits NADPH oxidase (NOX)-1 activation and NF-kappaB-dependent release of inflammatory mediators and prevents the increase of epithelial permeability in IL-1beta-exposed Caco-2 cells
    • Tesoriere L, Attanzio A, Allegra M, Gentile C, Livrea MA, Indicaxanthin inhibits NADPH oxidase (NOX)-1 activation and NF-kappaB-dependent release of inflammatory mediators and prevents the increase of epithelial permeability in IL-1beta-exposed Caco-2 cells, Br J Nutr 111:415-423, 2014.
    • (2014) Br J Nutr , vol.111 , pp. 415-423
    • Tesoriere, L.1    Attanzio, A.2    Allegra, M.3    Gentile, C.4    Livrea, M.A.5
  • 41
    • 80155147940 scopus 로고    scopus 로고
    • Expression of zinc finger protein A20 in pediatric inflammatory bowel disease
    • Zheng CF, Huang Y, Expression of zinc finger protein A20 in pediatric inflammatory bowel disease, Zhonghua Er Ke Za Zhi 49:261-265, 2011.
    • (2011) Zhonghua Er Ke Za Zhi , vol.49 , pp. 261-265
    • Zheng, C.F.1    Huang, Y.2
  • 42
    • 84869213229 scopus 로고    scopus 로고
    • Immune markers and differential signaling networks in ulcerative colitis and Crohn's disease
    • Christophi GP, Rong R, Holtzapple PG, Massa PT, Landas SK, Immune markers and differential signaling networks in ulcerative colitis and Crohn's disease, Inflamm Bowel Dis 18:2342-2356, 2012.
    • (2012) Inflamm Bowel Dis , vol.18 , pp. 2342-2356
    • Christophi, G.P.1    Rong, R.2    Holtzapple, P.G.3    Massa, P.T.4    Landas, S.K.5
  • 43
    • 84887062557 scopus 로고    scopus 로고
    • Janus kinase inhibition with tofacitinib: Changing the face of inflammatory bowel disease treatment
    • Vuitton L, Koch S, Peyrin-Biroulet L, Janus kinase inhibition with tofacitinib: Changing the face of inflammatory bowel disease treatment, Curr Drug Targets 14:1385-1391, 2013.
    • (2013) Curr Drug Targets , vol.14 , pp. 1385-1391
    • Vuitton, L.1    Koch, S.2    Peyrin-Biroulet, L.3
  • 44
    • 77749258191 scopus 로고    scopus 로고
    • Increased susceptibility to dextran sulfate sodium induced colitis in the T cell protein tyrosine phosphatase heterozygous mouse
    • Hassan SW, Doody KM, Hardy S, Uetani N, Cournoyer D, Tremblay ML, Increased susceptibility to dextran sulfate sodium induced colitis in the T cell protein tyrosine phosphatase heterozygous mouse, PLoS One 5:e8868, 2010.
    • (2010) PLoS One , vol.5
    • Hassan, S.W.1    Doody, K.M.2    Hardy, S.3    Uetani, N.4    Cournoyer, D.5    Tremblay, M.L.6
  • 45
    • 77955270391 scopus 로고    scopus 로고
    • Analysis of JAK2 and STAT3 polymorphisms in patients with ankylosing spondylitis in Chinese Han population
    • Chen C, Zhang X, Wang Y, Analysis of JAK2 and STAT3 polymorphisms in patients with ankylosing spondylitis in Chinese Han population, Clin Immunol 136:442-446, 2010.
    • (2010) Clin Immunol , vol.136 , pp. 442-446
    • Chen, C.1    Zhang, X.2    Wang, Y.3
  • 46
    • 42449133751 scopus 로고    scopus 로고
    • Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease
    • Carey R, Jurickova I, Ballard E, Bonkowski E, Han X, Xu H, Denson LA, Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease, Inflamm Bowel Dis 14:446-457, 2008.
    • (2008) Inflamm Bowel Dis , vol.14 , pp. 446-457
    • Carey, R.1    Jurickova, I.2    Ballard, E.3    Bonkowski, E.4    Han, X.5    Xu, H.6    Denson, L.A.7
  • 50
    • 36849042673 scopus 로고    scopus 로고
    • Opposing regulation of the tight junction protein claudin-2 by interferon-gamma and interleukin-4
    • Wisner DM, Harris LR, 3rd, Green CL, Poritz LS, Opposing regulation of the tight junction protein claudin-2 by interferon-gamma and interleukin-4, J Surg Res 144:1-7, 2008.
    • (2008) J Surg Res , vol.144 , pp. 1-7
    • Wisner, D.M.1    Harris III, L.R.2    Green, C.L.3    Poritz, L.S.4
  • 51
    • 84863009612 scopus 로고    scopus 로고
    • The JAK2 variant rs10758669 in Crohn's disease: Altering the intestinal barrier as one mechanism of action
    • Prager M, Buttner J, Haas V, Baumgart DC, Sturm A, Zeitz M, Buning C, The JAK2 variant rs10758669 in Crohn's disease: Altering the intestinal barrier as one mechanism of action, Int J Colorectal Dis 27:565-573, 2012.
    • (2012) Int J Colorectal Dis , vol.27 , pp. 565-573
    • Prager, M.1    Buttner, J.2    Haas, V.3    Baumgart, D.C.4    Sturm, A.5    Zeitz, M.6    Buning, C.7
  • 52
    • 84870404456 scopus 로고    scopus 로고
    • Association of IL-8 gene polymorphisms with inflammatory bowel disease in Chinese patients
    • Liang WD, Li JS, Li KS, Jin J, Yan J, Yang JF, Bi YT, Association of IL-8 gene polymorphisms with inflammatory bowel disease in Chinese patients, Zhonghua Yi Xue Za Zhi 91:1825-1829, 2011.
    • (2011) Zhonghua Yi Xue Za Zhi , vol.91 , pp. 1825-1829
    • Liang, W.D.1    Li, J.S.2    Li, K.S.3    Jin, J.4    Yan, J.5    Yang, J.F.6    Bi, Y.T.7
  • 53
    • 45749157250 scopus 로고    scopus 로고
    • Involvement of NF-kappaB in the inhibitory actions of Platycarya strobilacea on the TNF-alpha-induced monocyte adhesion to colon epithelial cells and chemokine expression
    • Babu D, Lee JS, Park SY, Thapa D, Choi MK, Kim AR, Park YJ, Kim JA, Involvement of NF-kappaB in the inhibitory actions of Platycarya strobilacea on the TNF-alpha-induced monocyte adhesion to colon epithelial cells and chemokine expression, Arch Pharm Res 31:727-735, 2008.
    • (2008) Arch Pharm Res , vol.31 , pp. 727-735
    • Babu, D.1    Lee, J.S.2    Park, S.Y.3    Thapa, D.4    Choi, M.K.5    Kim, A.R.6    Park, Y.J.7    Kim, J.A.8
  • 55
    • 0035080601 scopus 로고    scopus 로고
    • Role of T lymphocytes in rat 2 4 6-trinitrobenzene sulphonic acid (TNBS) induced colitis: Increased mortality after gammadelta T cell depletion and no effect of alphabeta T cell depletion
    • Hoffmann JC, Peters K, Henschke S, Herrmann B, Pfister K, Westermann J, Zeitz M, Role of T lymphocytes in rat 2, 4, 6-trinitrobenzene sulphonic acid (TNBS) induced colitis: Increased mortality after gammadelta T cell depletion and no effect of alphabeta T cell depletion, Gut 48:489-495, 2001.
    • (2001) Gut , vol.48 , pp. 489-495
    • Hoffmann, J.C.1    Peters, K.2    Henschke, S.3    Herrmann, B.4    Pfister, K.5    Westermann, J.6    Zeitz, M.7
  • 58
    • 79551622962 scopus 로고    scopus 로고
    • Analysis of IL2/IL21 gene variants in cholestatic liver diseases reveals an association with primary sclerosing cholangitis
    • Stallhofer J, Denk GU, Glas J, Laubender RP, Goke B, Rust C, Brand S, Pusl T, Analysis of IL2/IL21 gene variants in cholestatic liver diseases reveals an association with primary sclerosing cholangitis, Digestion 84:29-35, 2011.
    • (2011) Digestion , vol.84 , pp. 29-35
    • Stallhofer, J.1    Denk, G.U.2    Glas, J.3    Laubender, R.P.4    Goke, B.5    Rust, C.6    Brand, S.7    Pusl, T.8
  • 63
    • 84906678855 scopus 로고    scopus 로고
    • Liver Injury Secondary to anti-TNF-alpha therapy in inflammatory bowel disease: A case series and review of the literature
    • Parekh R, Kaur N, Liver Injury Secondary to anti-TNF-alpha therapy in inflammatory bowel disease: A case series and review of the literature, Case Rep Gastrointest Med 2014:956463, 2014.
    • (2014) Case Rep Gastrointest Med , vol.2014 , pp. 956463
    • Parekh, R.1    Kaur, N.2
  • 65
    • 84898538879 scopus 로고    scopus 로고
    • New biologics for treatment of chronic inflammatory bowel diseases
    • Schreiber S, Bachmann O, New biologics for treatment of chronic inflammatory bowel diseases, Internist (Berl) 55:367-376, 2014.
    • (2014) Internist (Berl) , vol.55 , pp. 367-376
    • Schreiber, S.1    Bachmann, O.2
  • 67
    • 84906657678 scopus 로고    scopus 로고
    • Polymorphisms of STAT4 and the risk of inflammatory bowel disease: A case-control study in Chinese Han population
    • Zhu H, Liu J, Zhang H, Wang Z, Lu S, Xu W, Zhong J, Polymorphisms of STAT4 and the risk of inflammatory bowel disease: A case-control study in Chinese Han population, Biomed Rep 1:320-324, 2013.
    • (2013) Biomed Rep , vol.1 , pp. 320-324
    • Zhu, H.1    Liu, J.2    Zhang, H.3    Wang, Z.4    Lu, S.5    Xu, W.6    Zhong, J.7
  • 68
    • 28844458016 scopus 로고    scopus 로고
    • Expression of chemokine receptors in normal and inflamed human intestine, tonsil, and liver-an immunohistochemical analysis with new monoclonal antibodies from the 8th international workshop and conference on human leucocyte differentiation antigens
    • Autschbach F, Funke B, Katzenmeier M, Gassler N, Expression of chemokine receptors in normal and inflamed human intestine, tonsil, and liver-an immunohistochemical analysis with new monoclonal antibodies from the 8th international workshop and conference on human leucocyte differentiation antigens, Cell Immunol 236:110-114, 2005.
    • (2005) Cell Immunol , vol.236 , pp. 110-114
    • Autschbach, F.1    Funke, B.2    Katzenmeier, M.3    Gassler, N.4
  • 73
    • 84882433613 scopus 로고    scopus 로고
    • Involvement of JAK/STAT signaling in the pathogenesis of inflammatory bowel disease
    • Coskun M, Salem M, Pedersen J, Nielsen OH, Involvement of JAK/STAT signaling in the pathogenesis of inflammatory bowel disease, Pharmacol Res 76:1-8, 2013.
    • (2013) Pharmacol Res , vol.76 , pp. 1-8
    • Coskun, M.1    Salem, M.2    Pedersen, J.3    Nielsen, O.H.4
  • 74
    • 58149232723 scopus 로고    scopus 로고
    • Role of STAT3 in inflammatory bowel disease
    • Sugimoto K, Role of STAT3 in inflammatory bowel disease, World J Gastroenterol 14:5110-5114, 2008.
    • (2008) World J Gastroenterol , vol.14 , pp. 5110-5114
    • Sugimoto, K.1


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