메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Identifying dysregulated pathways in cancers from pathway interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR PATHWAY; COMPLEX DISEASE; FEATURE SELECTION PROBLEM; FUNCTIONAL DEPENDENCY; GENE EXPRESSION DATA; MULTIPLE GENES; PATHOGENIC PATHWAYS; PATHWAY INTERACTIONS; POTENTIAL DRUG TARGETS; PROTEIN-PROTEIN INTERACTIONS; SMALL SAMPLE SIZE; STATE-OF-THE-ART METHODS; SUBNETWORKS; THREE FOLDS;

EID: 84861843896     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-126     Document Type: Article
Times cited : (108)

References (46)
  • 3
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
    • 10.1126/science.286.5439.531, 10521349
    • Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531-537. 10.1126/science.286.5439.531, 10521349.
    • (1999) Science , vol.286 , Issue.5439 , pp. 531-537
    • Golub, T.R.1    Slonim, D.K.2    Tamayo, P.3    Huard, C.4    Gaasenbeek, M.5    Mesirov, J.P.6    Coller, H.7    Loh, M.L.8    Downing, J.R.9    Caligiuri, M.A.10
  • 4
    • 0034911875 scopus 로고    scopus 로고
    • An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles
    • 10.1101/gr.165101, 311075, 11435405
    • Thomas JG, Olson JM, Tapscott SJ, Zhao LP. An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles. Genome Res 2001, 11(7):1227-1236. 10.1101/gr.165101, 311075, 11435405.
    • (2001) Genome Res , vol.11 , Issue.7 , pp. 1227-1236
    • Thomas, J.G.1    Olson, J.M.2    Tapscott, S.J.3    Zhao, L.P.4
  • 5
    • 0037093087 scopus 로고    scopus 로고
    • Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray
    • Han H, Bearss DJ, Browne LW, Calaluce R, Nagle RB, Von Hoff DD. Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. Cancer Res 2002, 62(10):2890-2896.
    • (2002) Cancer Res , vol.62 , Issue.10 , pp. 2890-2896
    • Han, H.1    Bearss, D.J.2    Browne, L.W.3    Calaluce, R.4    Nagle, R.B.5    Von Hoff, D.D.6
  • 6
    • 1342330535 scopus 로고    scopus 로고
    • Is cross-validation valid for small-sample microarray classification?
    • 10.1093/bioinformatics/btg419, 14960464
    • Braga-Neto UM, Dougherty ER. Is cross-validation valid for small-sample microarray classification?. Bioinformatics 2004, 20(3):374-380. 10.1093/bioinformatics/btg419, 14960464.
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 374-380
    • Braga-Neto, U.M.1    Dougherty, E.R.2
  • 7
    • 0035895515 scopus 로고    scopus 로고
    • Genomics and medicine. Dissecting human disease in the postgenomic era
    • 10.1126/science.291.5507.1224, 11233446
    • Peltonen L, McKusick VA. Genomics and medicine. Dissecting human disease in the postgenomic era. Science 2001, 291(5507):1224-1229. 10.1126/science.291.5507.1224, 11233446.
    • (2001) Science , vol.291 , Issue.5507 , pp. 1224-1229
    • Peltonen, L.1    McKusick, V.A.2
  • 9
    • 33745619786 scopus 로고    scopus 로고
    • Commentary: understanding sources of complexity in chronic diseases--the importance of integration of genetics and epidemiology
    • discussion 593-596, 10.1093/ije/dyl007, 16540533
    • Merikangas KR, Low NC, Hardy J. Commentary: understanding sources of complexity in chronic diseases--the importance of integration of genetics and epidemiology. Int J Epidemiol 2006, 35(3):590-592. discussion 593-596, 10.1093/ije/dyl007, 16540533.
    • (2006) Int J Epidemiol , vol.35 , Issue.3 , pp. 590-592
    • Merikangas, K.R.1    Low, N.C.2    Hardy, J.3
  • 10
    • 26444608611 scopus 로고    scopus 로고
    • Discovering statistically significant pathways in expression profiling studies
    • 10.1073/pnas.0506577102, 1200092, 16174746
    • Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A 2005, 102(38):13544-13549. 10.1073/pnas.0506577102, 1200092, 16174746.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.38 , pp. 13544-13549
    • Tian, L.1    Greenberg, S.A.2    Kong, S.W.3    Altschuler, J.4    Kohane, I.S.5    Park, P.J.6
  • 12
    • 35348891430 scopus 로고    scopus 로고
    • Network-based classification of breast cancer metastasis
    • 2063581, 17940530
    • Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol 2007, 3:140. 2063581, 17940530.
    • (2007) Mol Syst Biol , vol.3 , pp. 140
    • Chuang, H.Y.1    Lee, E.2    Liu, Y.T.3    Lee, D.4    Ideker, T.5
  • 13
    • 57149092133 scopus 로고    scopus 로고
    • Inferring pathway activity toward precise disease classification
    • 10.1371/journal.pcbi.1000217, 2563693, 18989396
    • Lee E, Chuang HY, Kim JW, Ideker T, Lee D. Inferring pathway activity toward precise disease classification. PLoS Comput Biol 2008, 4(11):e1000217. 10.1371/journal.pcbi.1000217, 2563693, 18989396.
    • (2008) PLoS Comput Biol , vol.4 , Issue.11
    • Lee, E.1    Chuang, H.Y.2    Kim, J.W.3    Ideker, T.4    Lee, D.5
  • 14
    • 84864288185 scopus 로고    scopus 로고
    • A pathway-based view of human diseases and disease relationships
    • 10.1371/journal.pone.0004346, 2631151, 19194489
    • Li Y, Agarwal P. A pathway-based view of human diseases and disease relationships. PLoS One 2009, 4(2):e4346. 10.1371/journal.pone.0004346, 2631151, 19194489.
    • (2009) PLoS One , vol.4 , Issue.2
    • Li, Y.1    Agarwal, P.2
  • 15
    • 77949524863 scopus 로고    scopus 로고
    • Accurate and reliable cancer classification based on probabilistic inference of pathway activity
    • 10.1371/journal.pone.0008161, 2781165, 19997592
    • Su J, Yoon BJ, Dougherty ER. Accurate and reliable cancer classification based on probabilistic inference of pathway activity. PLoS One 2009, 4(12):e8161. 10.1371/journal.pone.0008161, 2781165, 19997592.
    • (2009) PLoS One , vol.4 , Issue.12
    • Su, J.1    Yoon, B.J.2    Dougherty, E.R.3
  • 17
    • 78149460182 scopus 로고    scopus 로고
    • DEGAS: de novo discovery of dysregulated pathways in human diseases
    • 10.1371/journal.pone.0013367, 2957424, 20976054
    • Ulitsky I, Krishnamurthy A, Karp RM, Shamir R. DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS One 2010, 5(10):e13367. 10.1371/journal.pone.0013367, 2957424, 20976054.
    • (2010) PLoS One , vol.5 , Issue.10
    • Ulitsky, I.1    Krishnamurthy, A.2    Karp, R.M.3    Shamir, R.4
  • 18
    • 77956850355 scopus 로고    scopus 로고
    • Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains
    • 10.1186/1752-0509-4-S2-S11, 2982685, 20840725
    • Liu Z-P, Wang Y, Zhang X-S, Chen L. Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. BMC Syst Biol 2010, 4(Suppl 2):S11. 10.1186/1752-0509-4-S2-S11, 2982685, 20840725.
    • (2010) BMC Syst Biol , vol.4 , Issue.SUPPL. 2
    • Liu, Z.-P.1    Wang, Y.2    Zhang, X.-S.3    Chen, L.4
  • 19
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • 10.1093/nar/30.1.207, 99122, 11752295
    • Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-210. 10.1093/nar/30.1.207, 99122, 11752295.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 20
    • 33847749502 scopus 로고    scopus 로고
    • Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer
    • 10.1038/nm1556, 17334370
    • Spira A, Beane JE, Shah V, Steiling K, Liu G, Schembri F, Gilman S, Dumas YM, Calner P, Sebastiani P, et al. Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med 2007, 13(3):361-366. 10.1038/nm1556, 17334370.
    • (2007) Nat Med , vol.13 , Issue.3 , pp. 361-366
    • Spira, A.1    Beane, J.E.2    Shah, V.3    Steiling, K.4    Liu, G.5    Schembri, F.6    Gilman, S.7    Dumas, Y.M.8    Calner, P.9    Sebastiani, P.10
  • 21
    • 34249709906 scopus 로고    scopus 로고
    • Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process
    • 10.1186/1471-2407-7-64, 1865555, 17430594
    • Chandran UR, Ma C, Dhir R, Bisceglia M, Lyons-Weiler M, Liang W, Michalopoulos G, Becich M, Monzon FA. Gene expression profiles of prostate cancer reveal involvement of multiple molecular pathways in the metastatic process. BMC Cancer 2007, 7:64. 10.1186/1471-2407-7-64, 1865555, 17430594.
    • (2007) BMC Cancer , vol.7 , pp. 64
    • Chandran, U.R.1    Ma, C.2    Dhir, R.3    Bisceglia, M.4    Lyons-Weiler, M.5    Liang, W.6    Michalopoulos, G.7    Becich, M.8    Monzon, F.A.9
  • 23
    • 69249228672 scopus 로고    scopus 로고
    • FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt
    • 10.1016/j.ccr.2009.07.016, 2755578, 19732725
    • Pei H, Li L, Fridley BL, Jenkins GD, Kalari KR, Lingle W, Petersen G, Lou Z, Wang L. FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt. Cancer Cell 2009, 16(3):259-266. 10.1016/j.ccr.2009.07.016, 2755578, 19732725.
    • (2009) Cancer Cell , vol.16 , Issue.3 , pp. 259-266
    • Pei, H.1    Li, L.2    Fridley, B.L.3    Jenkins, G.D.4    Kalari, K.R.5    Lingle, W.6    Petersen, G.7    Lou, Z.8    Wang, L.9
  • 28
    • 58149421595 scopus 로고
    • Analysis of a Complex of Statistical Variables into Principal Components
    • Hotelling H. Analysis of a Complex of Statistical Variables into Principal Components. Journal of Educational Psychology 1933, 24(6):417-441.
    • (1933) Journal of Educational Psychology , vol.24 , Issue.6 , pp. 417-441
    • Hotelling, H.1
  • 30
    • 32844472295 scopus 로고    scopus 로고
    • Biomarker discovery, disease classification, and similarity query processing on high-throughput MS/MS data of inborn errors of metabolism
    • Baumgartner C, Baumgartner D. Biomarker discovery, disease classification, and similarity query processing on high-throughput MS/MS data of inborn errors of metabolism. J Biomol Screen 2006, 11(1):90-99.
    • (2006) J Biomol Screen , vol.11 , Issue.1 , pp. 90-99
    • Baumgartner, C.1    Baumgartner, D.2
  • 31
    • 81455138867 scopus 로고    scopus 로고
    • A filter-based feature selection approach for identifying potential biomarkers for lung cancer
    • 10.1186/2043-9113-1-11, 3164604, 21884628
    • Lee IH, Lushington GH, Visvanathan M. A filter-based feature selection approach for identifying potential biomarkers for lung cancer. J Clin Bioinforma 2011, 1(1):11. 10.1186/2043-9113-1-11, 3164604, 21884628.
    • (2011) J Clin Bioinforma , vol.1 , Issue.1 , pp. 11
    • Lee, I.H.1    Lushington, G.H.2    Visvanathan, M.3
  • 32
    • 28244499333 scopus 로고    scopus 로고
    • Analysis of orthologous gene expression between human pulmonary adenocarcinoma and a carcinogen-induced murine model
    • 10.1016/S0002-9440(10)61257-6, 1613183, 16314486
    • Stearman RS, Dwyer-Nield L, Zerbe L, Blaine SA, Chan Z, Bunn PA, Johnson GL, Hirsch FR, Merrick DT, Franklin WA, et al. Analysis of orthologous gene expression between human pulmonary adenocarcinoma and a carcinogen-induced murine model. Am J Pathol 2005, 167(6):1763-1775. 10.1016/S0002-9440(10)61257-6, 1613183, 16314486.
    • (2005) Am J Pathol , vol.167 , Issue.6 , pp. 1763-1775
    • Stearman, R.S.1    Dwyer-Nield, L.2    Zerbe, L.3    Blaine, S.A.4    Chan, Z.5    Bunn, P.A.6    Johnson, G.L.7    Hirsch, F.R.8    Merrick, D.T.9    Franklin, W.A.10
  • 33
    • 34347209095 scopus 로고    scopus 로고
    • Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme
    • 10.1186/1471-2164-8-140, 1894975, 17540040
    • Su LJ, Chang CW, Wu YC, Chen KC, Lin CJ, Liang SC, Lin CH, Whang-Peng J, Hsu SL, Chen CH, et al. Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics 2007, 8:140. 10.1186/1471-2164-8-140, 1894975, 17540040.
    • (2007) BMC Genomics , vol.8 , pp. 140
    • Su, L.J.1    Chang, C.W.2    Wu, Y.C.3    Chen, K.C.4    Lin, C.J.5    Liang, S.C.6    Lin, C.H.7    Whang-Peng, J.8    Hsu, S.L.9    Chen, C.H.10
  • 34
    • 45749140422 scopus 로고    scopus 로고
    • Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival
    • 10.1371/journal.pone.0001651, 2249927, 18297132
    • Landi MT, Dracheva T, Rotunno M, Figueroa JD, Liu H, Dasgupta A, Mann FE, Fukuoka J, Hames M, Bergen AW, et al. Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS One 2008, 3(2):e1651. 10.1371/journal.pone.0001651, 2249927, 18297132.
    • (2008) PLoS One , vol.3 , Issue.2
    • Landi, M.T.1    Dracheva, T.2    Rotunno, M.3    Figueroa, J.D.4    Liu, H.5    Dasgupta, A.6    Mann, F.E.7    Fukuoka, J.8    Hames, M.9    Bergen, A.W.10
  • 35
    • 77957821749 scopus 로고    scopus 로고
    • Genetic variation and antioxidant response gene expression in the bronchial airway epithelium of smokers at risk for lung cancer
    • 10.1371/journal.pone.0011934, 2914741, 20689807
    • Wang X, Chorley BN, Pittman GS, Kleeberger SR, Brothers J, Liu G, Spira A, Bell DA. Genetic variation and antioxidant response gene expression in the bronchial airway epithelium of smokers at risk for lung cancer. PLoS One 2010, 5(8):e11934. 10.1371/journal.pone.0011934, 2914741, 20689807.
    • (2010) PLoS One , vol.5 , Issue.8
    • Wang, X.1    Chorley, B.N.2    Pittman, G.S.3    Kleeberger, S.R.4    Brothers, J.5    Liu, G.6    Spira, A.7    Bell, D.A.8
  • 36
    • 70349442548 scopus 로고    scopus 로고
    • The first 30 years of p53: growing ever more complex
    • 10.1038/nrc2723, 2771725, 19776744
    • Levine AJ, Oren M. The first 30 years of p53: growing ever more complex. Nat Rev Cancer 2009, 9(10):749-758. 10.1038/nrc2723, 2771725, 19776744.
    • (2009) Nat Rev Cancer , vol.9 , Issue.10 , pp. 749-758
    • Levine, A.J.1    Oren, M.2
  • 37
    • 67749117934 scopus 로고    scopus 로고
    • Signal integration by JNK and p38 MAPK pathways in cancer development
    • 10.1038/nrc2694, 19629069
    • Wagner EF, Nebreda AR. Signal integration by JNK and p38 MAPK pathways in cancer development. Nat Rev Cancer 2009, 9(8):537-549. 10.1038/nrc2694, 19629069.
    • (2009) Nat Rev Cancer , vol.9 , Issue.8 , pp. 537-549
    • Wagner, E.F.1    Nebreda, A.R.2
  • 38
    • 53149122044 scopus 로고    scopus 로고
    • ERK and JNK mediate TNFalpha-induced p53 activation in apoptotic and autophagic L929 cell death
    • 10.1016/j.bbrc.2008.09.018, 18796294
    • Cheng Y, Qiu F, Tashiro S, Onodera S, Ikejima T. ERK and JNK mediate TNFalpha-induced p53 activation in apoptotic and autophagic L929 cell death. Biochem Biophys Res Commun 2008, 376(3):483-488. 10.1016/j.bbrc.2008.09.018, 18796294.
    • (2008) Biochem Biophys Res Commun , vol.376 , Issue.3 , pp. 483-488
    • Cheng, Y.1    Qiu, F.2    Tashiro, S.3    Onodera, S.4    Ikejima, T.5
  • 39
    • 0033596124 scopus 로고    scopus 로고
    • Aberrant rel/nfkb genes and activity in human cancer
    • 10.1038/sj.onc.1203221, 10602468
    • Rayet B, Gelinas C. Aberrant rel/nfkb genes and activity in human cancer. Oncogene 1999, 18(49):6938-6947. 10.1038/sj.onc.1203221, 10602468.
    • (1999) Oncogene , vol.18 , Issue.49 , pp. 6938-6947
    • Rayet, B.1    Gelinas, C.2
  • 40
    • 7044275192 scopus 로고    scopus 로고
    • Suppressed NF-kappaB and sustained JNK activation contribute to the sensitization effect of parthenolide to TNF-alpha-induced apoptosis in human cancer cells
    • 10.1093/carcin/bgh234, 15256485
    • Zhang S, Lin ZN, Yang CF, Shi X, Ong CN, Shen HM. Suppressed NF-kappaB and sustained JNK activation contribute to the sensitization effect of parthenolide to TNF-alpha-induced apoptosis in human cancer cells. Carcinogenesis 2004, 25(11):2191-2199. 10.1093/carcin/bgh234, 15256485.
    • (2004) Carcinogenesis , vol.25 , Issue.11 , pp. 2191-2199
    • Zhang, S.1    Lin, Z.N.2    Yang, C.F.3    Shi, X.4    Ong, C.N.5    Shen, H.M.6
  • 42
    • 0036632368 scopus 로고    scopus 로고
    • The phosphatidylinositol 3-Kinase AKT pathway in human cancer
    • 10.1038/nrc839, 12094235
    • Vivanco I, Sawyers CL. The phosphatidylinositol 3-Kinase AKT pathway in human cancer. Nat Rev Cancer 2002, 2(7):489-501. 10.1038/nrc839, 12094235.
    • (2002) Nat Rev Cancer , vol.2 , Issue.7 , pp. 489-501
    • Vivanco, I.1    Sawyers, C.L.2
  • 43
    • 9644253003 scopus 로고    scopus 로고
    • The PI 3-kinase/Akt signaling pathway is activated due to aberrant Pten expression and targets transcription factors NF-kappaB and c-Myc in pancreatic cancer cells
    • 10.1038/sj.onc.1207902, 15467756
    • Asano T, Yao Y, Zhu J, Li D, Abbruzzese JL, Reddy SA. The PI 3-kinase/Akt signaling pathway is activated due to aberrant Pten expression and targets transcription factors NF-kappaB and c-Myc in pancreatic cancer cells. Oncogene 2004, 23(53):8571-8580. 10.1038/sj.onc.1207902, 15467756.
    • (2004) Oncogene , vol.23 , Issue.53 , pp. 8571-8580
    • Asano, T.1    Yao, Y.2    Zhu, J.3    Li, D.4    Abbruzzese, J.L.5    Reddy, S.A.6
  • 44
  • 45
    • 82455188358 scopus 로고    scopus 로고
    • Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach
    • 10.1186/1471-2164-12-592, 3256240, 22136190
    • He D, Liu ZP, Chen L. Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. BMC Genomics 2011, 12:592. 10.1186/1471-2164-12-592, 3256240, 22136190.
    • (2011) BMC Genomics , vol.12 , pp. 592
    • He, D.1    Liu, Z.P.2    Chen, L.3
  • 46
    • 84859741480 scopus 로고    scopus 로고
    • Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers
    • 3314989, 22461973
    • Chen L, Liu R, Liu ZP, Li M, Aihara K. Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Sci Rep 2012, 2:342. 3314989, 22461973.
    • (2012) Sci Rep , vol.2 , pp. 342
    • Chen, L.1    Liu, R.2    Liu, Z.P.3    Li, M.4    Aihara, K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.