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Volumn 15, Issue 1, 2014, Pages

MAAMD: A workflow to standardize meta-analyses and comparison of affymetrix microarray data

Author keywords

Affymetrix microarray; AltAnalyze; Gene orthologues; Hypoxia; Kepler; Meta analysis; Workflow

Indexed keywords

BIOINFORMATICS; DATA VISUALIZATION; GENES; MAMMALS; PLANTS (BOTANY);

EID: 84897492562     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-69     Document Type: Article
Times cited : (11)

References (23)
  • 1
    • 78651491371 scopus 로고    scopus 로고
    • Microarray-based gene expression studies in ovarian cancer
    • Chon HS, Lancaster JM. Microarray-based gene expression studies in ovarian cancer. Canc Contr 2011, 18(1):8-15.
    • (2011) Canc Contr , vol.18 , Issue.1 , pp. 8-15
    • Chon, H.S.1    Lancaster, J.M.2
  • 2
    • 34547665469 scopus 로고    scopus 로고
    • Comparing microarray studies
    • 10.1007/978-1-59745-390-5_8, 17634614
    • Suarez-Farinas M, Magnasco MO. Comparing microarray studies. Methods Mol Biol 2007, 377:139-152. 10.1007/978-1-59745-390-5_8, 17634614.
    • (2007) Methods Mol Biol , vol.377 , pp. 139-152
    • Suarez-Farinas, M.1    Magnasco, M.O.2
  • 3
    • 84861793773 scopus 로고    scopus 로고
    • Gene set enrichment analysis:performance evaluation and usage guidelines
    • 10.1093/bib/bbr049, 3357488, 21900207
    • Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C. Gene set enrichment analysis:performance evaluation and usage guidelines. Brief Bioinform 2012, 13(3):281-291. 10.1093/bib/bbr049, 3357488, 21900207.
    • (2012) Brief Bioinform , vol.13 , Issue.3 , pp. 281-291
    • Hung, J.H.1    Yang, T.H.2    Hu, Z.3    Weng, Z.4    DeLisi, C.5
  • 4
    • 84872029236 scopus 로고    scopus 로고
    • Chapter 9:analyses using disease ontologies
    • 10.1371/journal.pcbi.1002827, 3531278, 23300417
    • Shah NH, Cole T, Musen MA. Chapter 9:analyses using disease ontologies. PLoS Comput Biol 2012, 8(12):e1002827. 10.1371/journal.pcbi.1002827, 3531278, 23300417.
    • (2012) PLoS Comput Biol , vol.8 , Issue.12
    • Shah, N.H.1    Cole, T.2    Musen, M.A.3
  • 6
    • 25444447098 scopus 로고    scopus 로고
    • Workflows in bioinformatics:meta-analysis and prototype implementation of a workflow generator
    • 10.1186/1471-2105-6-87, 1090554, 15813976
    • Garcia Castro A, Thoraval S, Garcia LJ, Ragan MA. Workflows in bioinformatics:meta-analysis and prototype implementation of a workflow generator. BMC Bioinformatics 2005, 6:87. 10.1186/1471-2105-6-87, 1090554, 15813976.
    • (2005) BMC Bioinformatics , vol.6 , pp. 87
    • Garcia Castro, A.1    Thoraval, S.2    Garcia, L.J.3    Ragan, M.A.4
  • 7
    • 33747109441 scopus 로고    scopus 로고
    • AMDA:an R package for the automated microarray data analysis
    • 10.1186/1471-2105-7-335, 1534071, 16824223
    • Pelizzola M, Pavelka N, Foti M, Ricciardi-Castagnoli P. AMDA:an R package for the automated microarray data analysis. BMC Bioinformatics 2006, 7:335. 10.1186/1471-2105-7-335, 1534071, 16824223.
    • (2006) BMC Bioinformatics , vol.7 , pp. 335
    • Pelizzola, M.1    Pavelka, N.2    Foti, M.3    Ricciardi-Castagnoli, P.4
  • 8
    • 84865098402 scopus 로고    scopus 로고
    • GO-Elite:a flexible solution for pathway and ontology over-representation
    • 10.1093/bioinformatics/bts366, 3413395, 22743224
    • Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N. GO-Elite:a flexible solution for pathway and ontology over-representation. Bioinformatics 2012, 28(16):2209-2210. 10.1093/bioinformatics/bts366, 3413395, 22743224.
    • (2012) Bioinformatics , vol.28 , Issue.16 , pp. 2209-2210
    • Zambon, A.C.1    Gaj, S.2    Ho, I.3    Hanspers, K.4    Vranizan, K.5    Evelo, C.T.6    Conklin, B.R.7    Pico, A.R.8    Salomonis, N.9
  • 10
    • 84861057273 scopus 로고    scopus 로고
    • Workflows for microarray data processing in the Kepler environment
    • 10.1186/1471-2105-13-102, 3431220, 22594911
    • Stropp T, McPhillips T, Ludascher B, Bieda M. Workflows for microarray data processing in the Kepler environment. BMC Bioinformatics 2012, 13:102. 10.1186/1471-2105-13-102, 3431220, 22594911.
    • (2012) BMC Bioinformatics , vol.13 , pp. 102
    • Stropp, T.1    McPhillips, T.2    Ludascher, B.3    Bieda, M.4
  • 12
    • 77954250511 scopus 로고    scopus 로고
    • AltAnalyze and DomainGraph:analyzing and visualizing exon expression data
    • 10.1093/nar/gkq405, 2896198, 20513647
    • Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M. AltAnalyze and DomainGraph:analyzing and visualizing exon expression data. Nucleic Acids Res 2010, 38:W755-W762. 10.1093/nar/gkq405, 2896198, 20513647.
    • (2010) Nucleic Acids Res , vol.38
    • Emig, D.1    Salomonis, N.2    Baumbach, J.3    Lengauer, T.4    Conklin, B.R.5    Albrecht, M.6
  • 13
    • 79952014397 scopus 로고    scopus 로고
    • Bioinformatics techniques in microarray research:applied microarray data analysis using R and SAS software
    • 10.1007/978-1-60761-820-1_25, 20717798
    • Demmer RT, Pavlidis P, Papapanou PN. Bioinformatics techniques in microarray research:applied microarray data analysis using R and SAS software. Methods Mol Biol 2010, 666:395-417. 10.1007/978-1-60761-820-1_25, 20717798.
    • (2010) Methods Mol Biol , vol.666 , pp. 395-417
    • Demmer, R.T.1    Pavlidis, P.2    Papapanou, P.N.3
  • 14
    • 69449095468 scopus 로고    scopus 로고
    • Hypoxia-induced mediators and neurologic disease
    • 10.1212/WNL.0b013e3181b2a719, 19687457
    • Benarroch EE. Hypoxia-induced mediators and neurologic disease. Neurology 2009, 73(7):560-565. 10.1212/WNL.0b013e3181b2a719, 19687457.
    • (2009) Neurology , vol.73 , Issue.7 , pp. 560-565
    • Benarroch, E.E.1
  • 15
    • 84887340602 scopus 로고    scopus 로고
    • The medical use of oxygen:a time for critical reappraisal
    • 10.1111/joim.12139, 24206183
    • Sjoberg F, Singer M. The medical use of oxygen:a time for critical reappraisal. J Intern Med 2013, 274(6):505-528. 10.1111/joim.12139, 24206183.
    • (2013) J Intern Med , vol.274 , Issue.6 , pp. 505-528
    • Sjoberg, F.1    Singer, M.2
  • 16
    • 78149433910 scopus 로고    scopus 로고
    • Chronic hypoxia impairs muscle function in the drosophila model of Duchenne's muscular dystrophy (DMD)
    • 10.1371/journal.pone.0013450, 2958114, 20975992
    • Mosqueira M, Willmann G, Ruohola-Baker H, Khurana TS. Chronic hypoxia impairs muscle function in the drosophila model of Duchenne's muscular dystrophy (DMD). Plos One 2010, 5(10):e13450. 10.1371/journal.pone.0013450, 2958114, 20975992.
    • (2010) Plos One , vol.5 , Issue.10
    • Mosqueira, M.1    Willmann, G.2    Ruohola-Baker, H.3    Khurana, T.S.4
  • 17
    • 65549159551 scopus 로고    scopus 로고
    • Distinct mechanisms underlying tolerance to intermittent and constant hypoxia in drosophila melanogaster
    • 10.1371/journal.pone.0005371, 2670512, 19401761
    • Azad P, Zhou D, Russo E, Haddad GG. Distinct mechanisms underlying tolerance to intermittent and constant hypoxia in drosophila melanogaster. Plos One 2009, 4(4):e5371. 10.1371/journal.pone.0005371, 2670512, 19401761.
    • (2009) Plos One , vol.4 , Issue.4
    • Azad, P.1    Zhou, D.2    Russo, E.3    Haddad, G.G.4
  • 18
    • 77955390642 scopus 로고    scopus 로고
    • Experimental selection for drosophila survival in extremely high O2 environments
    • 10.1371/journal.pone.0011701, 2909141, 20668515
    • Zhao HW, Zhou D, Nizet V, Haddad GG. Experimental selection for drosophila survival in extremely high O2 environments. Plos One 2010, 5(7):e11701. 10.1371/journal.pone.0011701, 2909141, 20668515.
    • (2010) Plos One , vol.5 , Issue.7
    • Zhao, H.W.1    Zhou, D.2    Nizet, V.3    Haddad, G.G.4
  • 19
    • 84866344659 scopus 로고    scopus 로고
    • Gene expression profiles of four heat shock proteins in response to different acute stresses in shrimp, Litopenaeus vannamei
    • Qian Z, Liu X, Wang L, Wang X, Li Y, Xiang J, Wang P. Gene expression profiles of four heat shock proteins in response to different acute stresses in shrimp, Litopenaeus vannamei. Comp Biochem Physiol Toxicol Pharmacol 2012, 156(3-4):211-220.
    • (2012) Comp Biochem Physiol Toxicol Pharmacol , vol.156 , Issue.3-4 , pp. 211-220
    • Qian, Z.1    Liu, X.2    Wang, L.3    Wang, X.4    Li, Y.5    Xiang, J.6    Wang, P.7
  • 20
    • 53149135477 scopus 로고    scopus 로고
    • Key issues in conducting a meta-analysis of gene expression microarray datasets
    • 10.1371/journal.pmed.0050184, 2528050, 18767902
    • Ramasamy A, Mondry A, Holmes CC, Altman DG. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS medicine 2008, 5(9):e184. 10.1371/journal.pmed.0050184, 2528050, 18767902.
    • (2008) PLoS medicine , vol.5 , Issue.9
    • Ramasamy, A.1    Mondry, A.2    Holmes, C.C.3    Altman, D.G.4
  • 21
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • 10.1093/biostatistics/kxj037, 16632515
    • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8(1):118-127. 10.1093/biostatistics/kxj037, 16632515.
    • (2007) Biostatistics , vol.8 , Issue.1 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 22
    • 77950949307 scopus 로고    scopus 로고
    • Dealing with missing values in large-scale studies:microarray data imputation and beyond
    • 10.1093/bib/bbp059, 19965979
    • Aittokallio T. Dealing with missing values in large-scale studies:microarray data imputation and beyond. Brief Bioinform 2010, 11(2):253-264. 10.1093/bib/bbp059, 19965979.
    • (2010) Brief Bioinform , vol.11 , Issue.2 , pp. 253-264
    • Aittokallio, T.1
  • 23
    • 79953089162 scopus 로고    scopus 로고
    • Meta-analysis of gene expression microarrays with missing replicates
    • 10.1186/1471-2105-12-84, 3224118, 21435268
    • Shi F, Abraham G, Leckie C, Haviv I, Kowalczyk A. Meta-analysis of gene expression microarrays with missing replicates. BMC Bioinformatics 2011, 12:84. 10.1186/1471-2105-12-84, 3224118, 21435268.
    • (2011) BMC Bioinformatics , vol.12 , pp. 84
    • Shi, F.1    Abraham, G.2    Leckie, C.3    Haviv, I.4    Kowalczyk, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.