메뉴 건너뛰기




Volumn 54, Issue 2, 2011, Pages 189-193

Functional modules with disease discrimination abilities for various cancers

Author keywords

[No Author keywords available]

Indexed keywords


EID: 79951570472     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-010-4129-7     Document Type: Article
Times cited : (2)

References (45)
  • 1
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher V G, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA, 2001, 98: 5116-5121.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 2
    • 33747344944 scopus 로고    scopus 로고
    • Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
    • Jeffery I B, Higgins D G, Culhane A C. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics, 2006, 7: 359.
    • (2006) BMC Bioinformatics , vol.7 , pp. 359
    • Jeffery, I.B.1    Higgins, D.G.2    Culhane, A.C.3
  • 3
    • 33947321935 scopus 로고    scopus 로고
    • Selection of differentially expressed genes in microarray data analysis
    • Chen J J, Wang S J, Tsai C A, et al. Selection of differentially expressed genes in microarray data analysis. Pharmacogenomics J, 2006.
    • (2006) Pharmacogenomics J
    • Chen, J.J.1    Wang, S.J.2    Tsai, C.A.3
  • 4
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • Cui X, Churchill G A. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol, 2003, 4: 210.
    • (2003) Genome Biol , vol.4 , pp. 210
    • Cui, X.1    Churchill, G.A.2
  • 5
    • 0141626917 scopus 로고    scopus 로고
    • The effect of replication on gene expression microarray experiments
    • Pavlidis P, Li Q, Noble W S. The effect of replication on gene expression microarray experiments. Bioinformatics, 2003, 19: 1620-1627.
    • (2003) Bioinformatics , vol.19 , pp. 1620-1627
    • Pavlidis, P.1    Li, Q.2    Noble, W.S.3
  • 6
    • 51749123784 scopus 로고    scopus 로고
    • Apparently low reproducibility of true differential expression discoveries in microarray studies
    • Zhang M, Yao C, Guo Z, et al. Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics, 2008, 24: 2057-2063.
    • (2008) Bioinformatics , vol.24 , pp. 2057-2063
    • Zhang, M.1    Yao, C.2    Guo, Z.3
  • 7
    • 33748495591 scopus 로고    scopus 로고
    • Rat toxicogenomic study reveals analytical consistency across microarray platforms
    • Guo L, Lobenhofer E K, Wang C, et al. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol, 2006, 24: 1162-1169.
    • (2006) Nat Biotechnol , vol.24 , pp. 1162-1169
    • Guo, L.1    Lobenhofer, E.K.2    Wang, C.3
  • 8
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    • Shi L, Reid L H, Jones W D, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol, 2006, 24: 1151-1161.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
    • Shi, L.1    Reid, L.H.2    Jones, W.D.3
  • 9
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: from disarray to consolidation and consensus
    • Allison D B, Cui X, Page G P, et al. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet, 2006, 7: 55-65.
    • (2006) Nat Rev Genet , vol.7 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3
  • 10
    • 25444476441 scopus 로고    scopus 로고
    • Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
    • Wolfe C J, Kohane I S, Butte A J. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics, 2005, 6: 227.
    • (2005) BMC Bioinformatics , vol.6 , pp. 227
    • Wolfe, C.J.1    Kohane, I.S.2    Butte, A.J.3
  • 11
    • 4344571581 scopus 로고    scopus 로고
    • Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    • Breitling R, Armengaud P, Amtmann A, et al. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett, 2004, 573: 83-92.
    • (2004) FEBS Lett , vol.573 , pp. 83-92
    • Breitling, R.1    Armengaud, P.2    Amtmann, A.3
  • 12
    • 38349188469 scopus 로고    scopus 로고
    • Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories
    • Yang D, Li Y, Xiao H, et al. Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories. Bioinformatics, 2008, 24: 265-271.
    • (2008) Bioinformatics , vol.24 , pp. 265-271
    • Yang, D.1    Li, Y.2    Xiao, H.3
  • 13
    • 13144305047 scopus 로고    scopus 로고
    • Systems biology for cancer
    • Khalil I G, Hill C. Systems biology for cancer. Curr Opin Oncol, 2005, 17: 44-48.
    • (2005) Curr Opin Oncol , vol.17 , pp. 44-48
    • Khalil, I.G.1    Hill, C.2
  • 14
    • 4043128071 scopus 로고    scopus 로고
    • Genetic analysis of genome-wide variation in human gene expression
    • Morley M, Molony C M, Weber T M, et al. Genetic analysis of genome-wide variation in human gene expression. Nature, 2004, 430: 743-747.
    • (2004) Nature , vol.430 , pp. 743-747
    • Morley, M.1    Molony, C.M.2    Weber, T.M.3
  • 15
    • 25444456388 scopus 로고    scopus 로고
    • Towards precise classification of cancers based on robust gene functional expression profiles
    • Guo Z, Zhang T, Li X, et al. Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics, 2005, 6: 58.
    • (2005) BMC Bioinformatics , vol.6 , pp. 58
    • Guo, Z.1    Zhang, T.2    Li, X.3
  • 16
    • 33846064113 scopus 로고    scopus 로고
    • NCBI GEO: mining tens of millions of expression profiles-database and tools update
    • Barrett T, Troup D B, Wilhite S E, et al. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res, 2007, 35: 760-765.
    • (2007) Nucleic Acids Res , vol.35 , pp. 760-765
    • Barrett, T.1    Troup, D.B.2    Wilhite, S.E.3
  • 17
    • 0035923583 scopus 로고    scopus 로고
    • Diversity of gene expression in adenocarcinoma of the lung
    • Garber M E, Troyanskaya O G, Schluens K, et al. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA, 2001, 98: 13784-13789.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 13784-13789
    • Garber, M.E.1    Troyanskaya, O.G.2    Schluens, K.3
  • 18
    • 0035923521 scopus 로고    scopus 로고
    • Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses
    • Bhattacharjee A, Richards W G, Staunton J, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA, 2001, 98: 13790-13795.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 13790-13795
    • Bhattacharjee, A.1    Richards, W.G.2    Staunton, J.3
  • 19
    • 50249185512 scopus 로고    scopus 로고
    • Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature
    • Galamb O, Gyorffy B, Sipos F, et al. Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature. Dis Markers, 2008, 25: 1-16.
    • (2008) Dis Markers , vol.25 , pp. 1-16
    • Galamb, O.1    Gyorffy, B.2    Sipos, F.3
  • 21
    • 9144251970 scopus 로고    scopus 로고
    • Gene expression profiling identifies clinically relevant subtypes of prostate cancer
    • Lapointe J, Li C, Higgins J P, et al. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA, 2004, 101: 811-816.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 811-816
    • Lapointe, J.1    Li, C.2    Higgins, J.P.3
  • 22
    • 12444313589 scopus 로고    scopus 로고
    • Variation in gene expression patterns in human gastric cancers
    • Chen X, Leung S Y, Yuen S T, et al. Variation in gene expression patterns in human gastric cancers. Mol Biol Cell, 2003, 14: 3208-3215.
    • (2003) Mol Biol Cell , vol.14 , pp. 3208-3215
    • Chen, X.1    Leung, S.Y.2    Yuen, S.T.3
  • 23
    • 4744347276 scopus 로고    scopus 로고
    • Novel endothelial cell markers in hepatocellular carcinoma
    • Chen X, Higgins J, Cheung S T, et al. Novel endothelial cell markers in hepatocellular carcinoma. Mod Pathol, 2004, 17: 1198-1210.
    • (2004) Mod Pathol , vol.17 , pp. 1198-1210
    • Chen, X.1    Higgins, J.2    Cheung, S.T.3
  • 24
    • 20044396570 scopus 로고    scopus 로고
    • Integrative analysis of the cancer transcriptome
    • Rhodes D R, Chinnaiyan A M. Integrative analysis of the cancer transcriptome. Nat Genet, 2005, 37: 31-37.
    • (2005) Nat Genet , vol.37 , pp. 31-37
    • Rhodes, D.R.1    Chinnaiyan, A.M.2
  • 25
    • 0037251963 scopus 로고    scopus 로고
    • SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
    • Diehn M, Sherlock G, Binkley G, et al. SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res, 2003, 31: 219-223.
    • (2003) Nucleic Acids Res , vol.31 , pp. 219-223
    • Diehn, M.1    Sherlock, G.2    Binkley, G.3
  • 26
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball C A, Blake J A, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000, 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 27
    • 0036489046 scopus 로고    scopus 로고
    • Comparison of discrimination methods for the classification of tumours using gene expression data
    • Dudoit S, Fridlyand J, Speed T. Comparison of discrimination methods for the classification of tumours using gene expression data. J Am Statisti Associ, 2002, 97: 77-87.
    • (2002) J Am Statisti Associ , vol.97 , pp. 77-87
    • Dudoit, S.1    Fridlyand, J.2    Speed, T.3
  • 28
    • 0037388166 scopus 로고    scopus 로고
    • Cell and tumor classification using gene expression data: construction of forests
    • Zhang H, Yu C Y, Singer B. Cell and tumor classification using gene expression data: construction of forests. Proc Natl Acad Sci USA, 2003, 100: 4168-4172.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 4168-4172
    • Zhang, H.1    Yu, C.Y.2    Singer, B.3
  • 29
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics, 2006, 22: 1600-1607.
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1    Rahnenfuhrer, J.2    Lengauer, T.3
  • 30
    • 33846689706 scopus 로고    scopus 로고
    • Using GOstats to test gene lists for GO term association
    • Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics, 2007, 23: 257-258.
    • (2007) Bioinformatics , vol.23 , pp. 257-258
    • Falcon, S.1    Gentleman, R.2
  • 31
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan D, Weinberg R A. The hallmarks of cancer. Cell, 2000, 100: 57-70.
    • (2000) Cell , vol.100 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 32
    • 33749051213 scopus 로고    scopus 로고
    • Can NF-kappaB be a target for novel and efficient anti-cancer agents?
    • Olivier S, Robe P, Bours V. Can NF-kappaB be a target for novel and efficient anti-cancer agents? Biochem Pharmacol, 2006, 72: 1054-1068.
    • (2006) Biochem Pharmacol , vol.72 , pp. 1054-1068
    • Olivier, S.1    Robe, P.2    Bours, V.3
  • 33
    • 55449118908 scopus 로고    scopus 로고
    • Nuclear factor kappa B: a marker of chemotherapy for human stage IV gastric carcinoma
    • Long Y M, Ye S, Rong J, et al. Nuclear factor kappa B: a marker of chemotherapy for human stage IV gastric carcinoma. World J Gastroenterol, 2008, 14: 4739-4744.
    • (2008) World J Gastroenterol , vol.14 , pp. 4739-4744
    • Long, Y.M.1    Ye, S.2    Rong, J.3
  • 34
    • 0028568315 scopus 로고
    • Cell cycle control and cancer
    • Hartwell L H, Kastan M B. Cell cycle control and cancer. Science, 1994, 266: 1821-1828.
    • (1994) Science , vol.266 , pp. 1821-1828
    • Hartwell, L.H.1    Kastan, M.B.2
  • 35
    • 0028556251 scopus 로고
    • Migration-associated volume changes in neutrophils facilitate the migratory process in vitro
    • Rosengren S, Henson P M, Worthen G S. Migration-associated volume changes in neutrophils facilitate the migratory process in vitro. Am J Physiol, 1994, 267: 1623-1632.
    • (1994) Am J Physiol , vol.267 , pp. 1623-1632
    • Rosengren, S.1    Henson, P.M.2    Worthen, G.S.3
  • 36
    • 30544447053 scopus 로고    scopus 로고
    • Involvement of aquaporin-4 in astroglial cell migration and glial scar formation
    • Saadoun S, Papadopoulos M C, Watanabe H, et al. Involvement of aquaporin-4 in astroglial cell migration and glial scar formation. J Cell Sci, 2005, 118: 5691-5698.
    • (2005) J Cell Sci , vol.118 , pp. 5691-5698
    • Saadoun, S.1    Papadopoulos, M.C.2    Watanabe, H.3
  • 37
    • 27844461512 scopus 로고    scopus 로고
    • Epithelial-mesenchymal transition in development and cancer: role of phosphatidylinositol 3′ kinase/AKT pathways
    • Larue L, Bellacosa A. Epithelial-mesenchymal transition in development and cancer: role of phosphatidylinositol 3′ kinase/AKT pathways. Oncogene, 2005, 24: 7443-7454.
    • (2005) Oncogene , vol.24 , pp. 7443-7454
    • Larue, L.1    Bellacosa, A.2
  • 38
    • 56749176437 scopus 로고    scopus 로고
    • Cadherins and cancer: how does cadherin dysfunction promote tumor progression?
    • Jeanes A, Gottardi C J, Yap A S. Cadherins and cancer: how does cadherin dysfunction promote tumor progression? Oncogene, 2008, 27: 6920-6929.
    • (2008) Oncogene , vol.27 , pp. 6920-6929
    • Jeanes, A.1    Gottardi, C.J.2    Yap, A.S.3
  • 39
    • 0037708932 scopus 로고    scopus 로고
    • Metastatic potential: generic predisposition of the primary tumor or rare, metastatic variants-or both?
    • Hynes R O. Metastatic potential: generic predisposition of the primary tumor or rare, metastatic variants-or both? Cell, 2003, 113: 821-823.
    • (2003) Cell , vol.113 , pp. 821-823
    • Hynes, R.O.1
  • 40
    • 0042967678 scopus 로고    scopus 로고
    • BMP-2 mediates retinoid-induced apoptosis in medulloblastoma cells through a paracrine effect
    • Hallahan A R, Pritchard J I, Chandraratna R A, et al. BMP-2 mediates retinoid-induced apoptosis in medulloblastoma cells through a paracrine effect. Nat Med, 2003, 9: 1033-1038.
    • (2003) Nat Med , vol.9 , pp. 1033-1038
    • Hallahan, A.R.1    Pritchard, J.I.2    Chandraratna, R.A.3
  • 41
    • 35348891430 scopus 로고    scopus 로고
    • Network-based classification of breast cancer metastasis
    • Chuang H Y, Lee E, Liu Y T, et al. Network-based classification of breast cancer metastasis. Mol Syst Biol, 2007, 3: 140.
    • (2007) Mol Syst Biol , vol.3 , pp. 140
    • Chuang, H.Y.1    Lee, E.2    Liu, Y.T.3
  • 42
    • 59849125136 scopus 로고    scopus 로고
    • Dynamic modularity in protein interaction networks predicts breast cancer outcome
    • Taylor I W, Linding R, Warde-Farley D, et al. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol, 2009, 27: 199-204.
    • (2009) Nat Biotechnol , vol.27 , pp. 199-204
    • Taylor, I.W.1    Linding, R.2    Warde-Farley, D.3
  • 43
    • 67649205714 scopus 로고    scopus 로고
    • Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
    • Zhang M, Zhang L, Zou J, et al. Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes. Bioinformatics, 2009, 25: 1662-1668.
    • (2009) Bioinformatics , vol.25 , pp. 1662-1668
    • Zhang, M.1    Zhang, L.2    Zou, J.3
  • 44
    • 6944244084 scopus 로고    scopus 로고
    • A module map showing conditional activity of expression modules in cancer
    • Segal E, Friedman N, Koller D, et al. A module map showing conditional activity of expression modules in cancer. Nat Genet, 2004, 36: 1090-1098.
    • (2004) Nat Genet , vol.36 , pp. 1090-1098
    • Segal, E.1    Friedman, N.2    Koller, D.3
  • 45
    • 33750937598 scopus 로고    scopus 로고
    • Mining expressed sequence tags identifies cancer markers of clinical interest
    • Campagne F, Skrabanek L. Mining expressed sequence tags identifies cancer markers of clinical interest. BMC Bioinformatics, 2006, 7: 481.
    • (2006) BMC Bioinformatics , vol.7 , pp. 481
    • Campagne, F.1    Skrabanek, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.