메뉴 건너뛰기




Volumn 9, Issue , 2008, Pages

Missing value imputation for microarray gene expression data using histone acetylation information

Author keywords

[No Author keywords available]

Indexed keywords

EXTERNAL INFORMATIONS; FUNCTIONAL SIMILARITY; IMPUTATION ALGORITHM; MICROARRAY GENE EXPRESSION DATA; MISSING VALUE IMPUTATION; PEARSON CORRELATION COEFFICIENTS; REGULATORY MECHANISM; ROOT MEAN SQUARED ERRORS;

EID: 46049116474     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-252     Document Type: Article
Times cited : (40)

References (54)
  • 8
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • 9843981
    • Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci U S A 1999, 95(25):10863-10868. 9843981
    • (1999) Proc Natl Acad Sci U S A , vol.95 , Issue.25 , pp. 10863-10868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 10
    • 0033657261 scopus 로고    scopus 로고
    • Principal components analysis to summarize microarray experiments: Application to sporulation time series
    • 10902193
    • Raychaudhuri S Stuart JM Altman RB Principal components analysis to summarize microarray experiments: Application to sporulation time series Pac Symp Biocomput 2000:455-466. 10902193
    • (2000) Pac Symp Biocomput , pp. 455-466
    • Raychaudhuri, S.1    Stuart, J.M.2    Altman, R.B.3
  • 11
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • 27718 10963673
    • Alter O Brown PO Botstein D Singular value decomposition for genome-wide expression data processing and modeling Proc Natl Acad Sci USA 2000, 97(18):10101-10106. 27718 10963673
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.18 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 12
    • 0037452966 scopus 로고    scopus 로고
    • Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms
    • 152296 12631705
    • Alter O Brown PO Botstein D Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms Proc Natl Acad Sci USA 2003, 100(6):3351-3356. 152296 12631705
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.6 , pp. 3351-3356
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 13
    • 33644856110 scopus 로고    scopus 로고
    • Improving missing value estimation in microarray data with gene ontology
    • 16377613
    • Tuikkala J Elo L Nevalainen OS Aittokallio T Improving missing value estimation in microarray data with gene ontology Bioinformatics 2006, 22(5):566-572. 16377613
    • (2006) Bioinformatics , vol.22 , Issue.5 , pp. 566-572
    • Tuikkala, J.1    Elo, L.2    Nevalainen, O.S.3    Aittokallio, T.4
  • 14
    • 2342426727 scopus 로고    scopus 로고
    • Gaussian mixture clustering and imputation of microarray data
    • 14751970
    • Ouyang M Welsh WJ Georgopoulos P Gaussian mixture clustering and imputation of microarray data Bioinformatics 2004, 20(6):917-923. 14751970
    • (2004) Bioinformatics , vol.20 , Issue.6 , pp. 917-923
    • Ouyang, M.1    Welsh, W.J.2    Georgopoulos, P.3
  • 18
    • 85047673373 scopus 로고    scopus 로고
    • Missing data: Our view of the state of the art
    • 12090408
    • Schafer JL Graham JW Missing data: Our view of the state of the art Psychol Methods 2002, 2(7):147-177. 12090408
    • (2002) Psychol Methods , vol.2 , Issue.7 , pp. 147-177
    • Schafer, J.L.1    Graham, J.W.2
  • 20
    • 33745615413 scopus 로고    scopus 로고
    • Missing value estimation for DNA microarray gene expression data: Local least squares imputation
    • Kim H Golub GH Park H Missing value estimation for DNA microarray gene expression data: Local least squares imputation Bioinformatics 2006, 22(11):1410-1411.
    • (2006) Bioinformatics , vol.22 , Issue.11 , pp. 1410-1411
    • Kim, H.1    Golub, G.H.2    Park, H.3
  • 21
    • 0242643743 scopus 로고    scopus 로고
    • A Bayesian missing value estimation method for gene expression profile data
    • 14594714
    • Oba S Sato M Takemasa I Monden M Matsubara K Ishii S A Bayesian missing value estimation method for gene expression profile data Bioinformatics 2003, 19(16):2088-2096. 14594714
    • (2003) Bioinformatics , vol.19 , Issue.16 , pp. 2088-2096
    • Oba, S.1    Sato, M.2    Takemasa, I.3    Monden, M.4    Matsubara, K.5    Ishii, S.6
  • 22
    • 33745714800 scopus 로고    scopus 로고
    • Collateral missing value estimation: Robust missing value estimation for consequent microarray data processing
    • Berlin: Springer-Verlag Berlin
    • Sehgal MSB Gondal I Dooley L Collateral missing value estimation: Robust missing value estimation for consequent microarray data processing Ai 2005: Advances In Artificial Intelligence Berlin: Springer-Verlag Berlin 2005, 3809:274-283.
    • (2005) Ai 2005: Advances In Artificial Intelligence , vol.3809 , pp. 274-283
    • Sehgal, M.S.B.1    Gondal, I.2    Dooley, L.3
  • 23
    • 33746974277 scopus 로고    scopus 로고
    • Improving missing value imputation of microarray data by using spot quality weights
    • 1533869 16780582
    • Johansson P Hakkinen J Improving missing value imputation of microarray data by using spot quality weights BMC Bioinformatics 2006, 7. 1533869 16780582
    • (2006) BMC Bioinformatics , vol.7
    • Johansson, P.1    Hakkinen, J.2
  • 25
    • 0037423930 scopus 로고    scopus 로고
    • Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin
    • 12628191
    • Meneghini MD Wu M Madhani HD Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin Cell 2003, 112:725-736. 12628191
    • (2003) Cell , vol.112 , pp. 725-736
    • Meneghini, M.D.1    Wu, M.2    Madhani, H.D.3
  • 27
    • 33748753680 scopus 로고    scopus 로고
    • Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae
    • Yuan GC Ma P Zhong WX Liu JS Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae Genome Biol 2006, 7:8.
    • (2006) Genome Biol , vol.7 , pp. 8
    • Yuan, G.C.1    Ma, P.2    Zhong, W.X.3    Liu, J.S.4
  • 31
    • 34047274419 scopus 로고    scopus 로고
    • Global patterns of histone modifications
    • 17317148
    • Rando OJ Global patterns of histone modifications Curr Opin Genet Dev 2007, 17:94-99. 17317148
    • (2007) Curr Opin Genet Dev , vol.17 , pp. 94-99
    • Rando, O.J.1
  • 32
    • 24744433805 scopus 로고    scopus 로고
    • Role of histone acetylation in the control of gene expression
    • 15959560
    • Verdone L Caserta M Di Mauro E Role of histone acetylation in the control of gene expression Biochem Cell Biol 2005, 83(3):344-353. 15959560
    • (2005) Biochem Cell Biol , vol.83 , Issue.3 , pp. 344-353
    • Verdone, L.1    Caserta, M.2    Di Mauro, E.3
  • 34
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
    • 9381177
    • DeRisi JL Iyer VR Brown PO Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale Science 1997, 278:680-686. 9381177
    • (1997) Science , vol.278 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 35
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • 25624 9843569
    • Spellman P Sherlock G Zhang M Iyer V Anders K Eisen M Brown P Botstein D Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 1998, 9:3273-3297. 25624 9843569
    • (1998) Mol Biol Cell , vol.9 , pp. 3273-3297
    • Spellman, P.1    Sherlock, G.2    Zhang, M.3    Iyer, V.4    Anders, K.5    Eisen, M.6    Brown, P.7    Botstein, D.8    Futcher, B.9
  • 36
    • 0037163129 scopus 로고    scopus 로고
    • Genome-wide analysis of gene expression regulated by the calcineurin/ Crz1p signaling pathway in Saccharomyces cerevisiae
    • 12058033
    • Yoshimoto H Saltsman K Gasch AP Li HX Ogawa N Botstein D Brown PO Cyert MS Genome-wide analysis of gene expression regulated by the calcineurin/ Crz1p signaling pathway in Saccharomyces cerevisiae J Biol Chem 2002, 277(34):31079-31088. 12058033
    • (2002) J Biol Chem , vol.277 , Issue.34 , pp. 31079-31088
    • Yoshimoto, H.1    Saltsman, K.2    Gasch, A.P.3    Li, H.X.4    Ogawa, N.5    Botstein, D.6    Brown, P.O.7    Cyert, M.S.8
  • 37
    • 2942518343 scopus 로고    scopus 로고
    • Mapping global histone acetylation patterns to gene expression
    • 15186774
    • Kurdistani SK Tavazoie S Grunstein M Mapping global histone acetylation patterns to gene expression Cell 2004, 117(6):721-733. 15186774
    • (2004) Cell , vol.117 , Issue.6 , pp. 721-733
    • Kurdistani, S.K.1    Tavazoie, S.2    Grunstein, M.3
  • 38
    • 34547909911 scopus 로고    scopus 로고
    • ChromatinDB: A database of genome-wide histone modification patterns for Saccharomyces cerevisiae
    • 17485428
    • O'Connor TR Wyrick JJ ChromatinDB: A database of genome-wide histone modification patterns for Saccharomyces cerevisiae Bioinformatics 2007, 23(14):1828-1830. 17485428
    • (2007) Bioinformatics , vol.23 , Issue.14 , pp. 1828-1830
    • O'Connor, T.R.1    Wyrick, J.J.2
  • 39
    • 33644837749 scopus 로고    scopus 로고
    • The Histone Database: A Comprehensive Resource for Histones and Histone Fold-Containing Proteins
    • 1800941 16345076
    • Mariño-Ramírez L Hsu B Baxevanis AD Landsman D The Histone Database: A Comprehensive Resource for Histones and Histone Fold-Containing Proteins Proteins 2006, 62(4):838-842. 1800941 16345076
    • (2006) Proteins , vol.62 , Issue.4 , pp. 838-842
    • Mariño-Ramírez, L.1    Hsu, B.2    Baxevanis, A.D.3    Landsman, D.4
  • 41
    • 18844413266 scopus 로고    scopus 로고
    • Acetylation in histone H3 globular domain regulates gene expression in yeast
    • 15882620
    • Feng X Zhang KL Grunstein M Acetylation in histone H3 globular domain regulates gene expression in yeast Cell 2005, 121(3):375-385. 15882620
    • (2005) Cell , vol.121 , Issue.3 , pp. 375-385
    • Feng, X.1    Zhang, K.L.2    Grunstein, M.3
  • 42
    • 46049085129 scopus 로고    scopus 로고
    • Sequence features of DNA binding sites reveal structural class of associated transcription factor
    • 16267080
    • Narlikar L Hartemink A Sequence features of DNA binding sites reveal structural class of associated transcription factor Bioinformatics 2005. 16267080
    • (2005) Bioinformatics
    • Narlikar, L.1    Hartemink, A.2
  • 44
    • 33747878866 scopus 로고    scopus 로고
    • Histone modification and regulation of chromatin function
    • Koryakov DE Histone modification and regulation of chromatin function Russ J Genet 2006, 42(9):970-984.
    • (2006) Russ J Genet , vol.42 , Issue.9 , pp. 970-984
    • Koryakov, D.E.1
  • 45
    • 33846006550 scopus 로고    scopus 로고
    • Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns
    • 1716270 17135569
    • Roh TY Wei G Farrell CM Zhao K Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns Genome Res 2007, 17(1):74-81. 1716270 17135569
    • (2007) Genome Res , vol.17 , Issue.1 , pp. 74-81
    • Roh, T.Y.1    Wei, G.2    Farrell, C.M.3    Zhao, K.4
  • 46
    • 33847380721 scopus 로고    scopus 로고
    • Histone acetylation and chromatin pattern in cancer - A review
    • 17375871
    • Orr JA Hamilton PW Histone acetylation and chromatin pattern in cancer - A review Anal Quant Cytol Histol 2007, 29(1):17-31. 17375871
    • (2007) Anal Quant Cytol Histol , vol.29 , Issue.1 , pp. 17-31
    • Orr, J.A.1    Hamilton, P.W.2
  • 47
    • 32544456936 scopus 로고    scopus 로고
    • Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae
    • 16339282
    • Guo X Tatsuoka K Liu RX Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae Bioinformatics 2006, 22(4):392-399. 16339282
    • (2006) Bioinformatics , vol.22 , Issue.4 , pp. 392-399
    • Guo, X.1    Tatsuoka, K.2    Liu, R.X.3
  • 48
    • 13244298228 scopus 로고    scopus 로고
    • Reuse of imputed data in microarray analysis increases imputation efficiency
    • Kim KJ Kim BJ Yi GS Reuse of imputed data in microarray analysis increases imputation efficiency BMC Bioinformatics 2004, 5.
    • (2004) BMC Bioinformatics , vol.5
    • Kim, K.J.1    Kim, B.J.2    Yi, G.S.3
  • 49
    • 0042706147 scopus 로고    scopus 로고
    • Genomic analysis of gene expression relationships in transcriptional regulatory networks
    • 12902159
    • Yu HY Luscombe NM Qian J Gerstein M Genomic analysis of gene expression relationships in transcriptional regulatory networks Trends Genet 2003, 19(8):422-427. 12902159
    • (2003) Trends Genet , vol.19 , Issue.8 , pp. 422-427
    • Yu, H.Y.1    Luscombe, N.M.2    Qian, J.3    Gerstein, M.4
  • 50
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • 12740579
    • Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data Nature Genet 2003, 34(2):166-176. 12740579
    • (2003) Nature Genet , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 51
    • 33746457753 scopus 로고    scopus 로고
    • Enhanced histone acetylation and transcription: A dynamic perspective
    • 16885019
    • Clayton AL Hazzalin CA Mahadevan LC Enhanced histone acetylation and transcription: A dynamic perspective Mol Cell 2006, 23(3):289-296. 16885019
    • (2006) Mol Cell , vol.23 , Issue.3 , pp. 289-296
    • Clayton, A.L.1    Hazzalin, C.A.2    Mahadevan, L.C.3
  • 52
    • 34250370970 scopus 로고    scopus 로고
    • The role of histone acetylation in regulating early gene expression patterns during early embryonic stem cell differentiation
    • 17204470
    • McCool KW Xu XJ Singer DB Murdoch FE Fritsch MK The role of histone acetylation in regulating early gene expression patterns during early embryonic stem cell differentiation J Biol Chem 2007, 282(9):6696-6706. 17204470
    • (2007) J Biol Chem , vol.282 , Issue.9 , pp. 6696-6706
    • McCool, K.W.1    Xu, X.J.2    Singer, D.B.3    Murdoch, F.E.4    Fritsch, M.K.5
  • 54
    • 84886758363 scopus 로고    scopus 로고
    • A Non-Parametric EM-Style Algorithm for Imputing Missing Values
    • Rich C A Non-Parametric EM-Style Algorithm for Imputing Missing Values AI and Statistics 2001.
    • (2001) AI and Statistics
    • Rich, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.