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Volumn 11, Issue , 2010, Pages

Predicting gene function using hierarchical multi-label decision tree ensembles

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; COMPUTATIONALLY EFFICIENT; FUNCTION PREDICTION; MACHINE LEARNING METHODS; PREDICTIVE PERFORMANCE; STATISTICAL LEARNING; STATISTICAL LEARNING METHODS; TREE-BASED METHODS;

EID: 77349119213     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-2     Document Type: Article
Times cited : (156)

References (44)
  • 2
    • 0038492417 scopus 로고    scopus 로고
    • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces Cerevisiae)
    • Troyanskaya O, Dolinski K, Owen A, Altman R, D B. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces Cerevisiae). Proceedings of the National Academy of Sciences 2003, 100(14):8348-8353.
    • (2003) Proceedings of the National Academy of Sciences , vol.100 , Issue.14 , pp. 8348-8353
    • Troyanskaya, O.1    Dolinski, K.2    Owen, A.3    Altman, R.4    D, B.5
  • 3
    • 6944251719 scopus 로고    scopus 로고
    • Predicting gene function in Saccharomyces cerevisiae
    • Clare A, King RD. Predicting gene function in Saccharomyces cerevisiae. Bioinformatics 2003, 19(Suppl 2):ii42-49.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Clare, A.1    King, R.D.2
  • 4
    • 13444283846 scopus 로고    scopus 로고
    • Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae
    • 10.1093/nar/gkh978, 535686, 15585665
    • Chen Y, Xu D. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Research 2004, 32(21):6414-6424. 10.1093/nar/gkh978, 535686, 15585665.
    • (2004) Nucleic Acids Research , vol.32 , Issue.21 , pp. 6414-6424
    • Chen, Y.1    Xu, D.2
  • 7
    • 15944404663 scopus 로고    scopus 로고
    • GOTrees: Predicting GO associations from protein domain composition using decision trees
    • World Scientific, Altman RB, Jung TA, Klein TE, Dunker AK, Hunter L, full_text, 15759620
    • Hayete B, Bienkowska J. GOTrees: Predicting GO associations from protein domain composition using decision trees. Pacific Symposium on Biocomputing 2005, 127-138. World Scientific, Altman RB, Jung TA, Klein TE, Dunker AK, Hunter L, full_text, 15759620.
    • (2005) Pacific Symposium on Biocomputing , pp. 127-138
    • Hayete, B.1    Bienkowska, J.2
  • 8
    • 33745619564 scopus 로고    scopus 로고
    • Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
    • 10.1093/bioinformatics/btl145, 16632496
    • Chua H, Sung W, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22(13):1623-1630. 10.1093/bioinformatics/btl145, 16632496.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1623-1630
    • Chua, H.1    Sung, W.2    Wong, L.3
  • 9
    • 33646151629 scopus 로고    scopus 로고
    • Functional bioinformatics for Arabidopsis thaliana
    • 10.1093/bioinformatics/btl051, 16481336
    • Clare A, Karwath A, Ougham H, King RD. Functional bioinformatics for Arabidopsis thaliana. Bioinformatics 2006, 22(9):1130-1136. 10.1093/bioinformatics/btl051, 16481336.
    • (2006) Bioinformatics , vol.22 , Issue.9 , pp. 1130-1136
    • Clare, A.1    Karwath, A.2    Ougham, H.3    King, R.D.4
  • 10
    • 33645323768 scopus 로고    scopus 로고
    • Hierarchical multi-label prediction of gene function
    • 10.1093/bioinformatics/btk048, 16410319
    • Barutcuoglu Z, Schapire R, Troyanskaya O. Hierarchical multi-label prediction of gene function. Bioinformatics 2006, 22(7):830-836. 10.1093/bioinformatics/btk048, 16410319.
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 830-836
    • Barutcuoglu, Z.1    Schapire, R.2    Troyanskaya, O.3
  • 13
    • 33645901213 scopus 로고    scopus 로고
    • Diffusion kernel-based logistic regression models for protein function prediction
    • 10.1089/omi.2006.10.40, 16584317
    • Lee H, Tu Z, Deng M, Sun F, Chen T. Diffusion kernel-based logistic regression models for protein function prediction. OMICS 2006, 10:40-55. 10.1089/omi.2006.10.40, 16584317.
    • (2006) OMICS , vol.10 , pp. 40-55
    • Lee, H.1    Tu, Z.2    Deng, M.3    Sun, F.4    Chen, T.5
  • 15
    • 47549107689 scopus 로고    scopus 로고
    • GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
    • 10.1186/gb-2008-9-s1-s4, 2447538, 18613948
    • Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biology 2008, 9(Suppl 1):S4. 10.1186/gb-2008-9-s1-s4, 2447538, 18613948.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 1
    • Mostafavi, S.1    Ray, D.2    Warde-Farley, D.3    Grouios, C.4    Morris, Q.5
  • 16
    • 47549098627 scopus 로고    scopus 로고
    • Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy
    • 10.1186/gb-2008-9-s1-s5, 2447539, 18613949
    • Kim W, Krumpelman C, Marcotte E. Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biology 2008, 9(Suppl 1):S5. 10.1186/gb-2008-9-s1-s5, 2447539, 18613949.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 1
    • Kim, W.1    Krumpelman, C.2    Marcotte, E.3
  • 17
    • 47549104748 scopus 로고    scopus 로고
    • Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
    • 10.1186/gb-2008-9-s1-s7, 2447541, 18613951
    • Tian W, Zhang L, Tasan M, Gibbons F, King O, Park J, Wunderlich Z, Cherry J, Roth F. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biology 2008, 9(Suppl 1):S7. 10.1186/gb-2008-9-s1-s7, 2447541, 18613951.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 1
    • Tian, W.1    Zhang, L.2    Tasan, M.3    Gibbons, F.4    King, O.5    Park, J.6    Wunderlich, Z.7    Cherry, J.8    Roth, F.9
  • 18
    • 47549108100 scopus 로고    scopus 로고
    • Predicting gene function in a hierarchical context with an ensemble of classifiers
    • 10.1186/gb-2008-9-s1-s3, 2447537, 18613947
    • Guan Y, Myers C, Hess D, Barutcuoglu Z, Caudy A, Troyanskaya O. Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biology 2008, 9(Suppl 1):S3. 10.1186/gb-2008-9-s1-s3, 2447537, 18613947.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 1
    • Guan, Y.1    Myers, C.2    Hess, D.3    Barutcuoglu, Z.4    Caudy, A.5    Troyanskaya, O.6
  • 19
    • 47549088657 scopus 로고    scopus 로고
    • Consistent probabilistic outputs for protein function prediction
    • 10.1186/gb-2008-9-s1-s6, 2447540, 18613950
    • Obozinski G, Lanckriet G, Grant C, Jordan M, Noble W. Consistent probabilistic outputs for protein function prediction. Genome Biology 2008, 9(Suppl 1):S6. 10.1186/gb-2008-9-s1-s6, 2447540, 18613950.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 1
    • Obozinski, G.1    Lanckriet, G.2    Grant, C.3    Jordan, M.4    Noble, W.5
  • 20
    • 0003500248 scopus 로고
    • Morgan Kaufmann series in Machine Learning, Morgan Kaufmann, Springer Netherlands
    • Quinlan J. C4.5: Programs for Machine Learning 1993, Morgan Kaufmann series in Machine Learning, Morgan Kaufmann, Springer Netherlands.
    • (1993) C4.5: Programs for Machine Learning
    • Quinlan, J.1
  • 21
    • 47549098812 scopus 로고    scopus 로고
    • A race through the maze of genomic evidence
    • 10.1186/gb-2008-9-s1-s1, 2447543, 18613945
    • Hughes T, Roth F. A race through the maze of genomic evidence. Genome Biology 2008, 9(Suppl 1):S1. 10.1186/gb-2008-9-s1-s1, 2447543, 18613945.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 1
    • Hughes, T.1    Roth, F.2
  • 23
    • 25844463253 scopus 로고    scopus 로고
    • Machine learning and data mining for yeast functional genomics
    • University of Wales, Aberystwyth, Computer Science Department
    • Clare A. Machine learning and data mining for yeast functional genomics. PhD thesis 2003, University of Wales, Aberystwyth, Computer Science Department.
    • (2003) PhD thesis
    • Clare, A.1
  • 30
  • 32
    • 0030211964 scopus 로고    scopus 로고
    • Bagging predictors
    • Breiman L. Bagging predictors. Machine Learning 1996, 24(2):123-140.
    • (1996) Machine Learning , vol.24 , Issue.2 , pp. 123-140
    • Breiman, L.1
  • 33
    • 0031189914 scopus 로고    scopus 로고
    • Multitask Learning
    • Caruana R. Multitask Learning. Machine Learning 1997, 28:41-75.
    • (1997) Machine Learning , vol.28 , pp. 41-75
    • Caruana, R.1
  • 36
    • 0033933636 scopus 로고    scopus 로고
    • Cascaded multiple classifiers for secondary structure prediction
    • 10.1110/ps.9.6.1162, 2144653, 10892809
    • Ouali M, King R. Cascaded multiple classifiers for secondary structure prediction. Protein Science 2000, 9(6):1162-76. 10.1110/ps.9.6.1162, 2144653, 10892809.
    • (2000) Protein Science , vol.9 , Issue.6 , pp. 1162-1176
    • Ouali, M.1    King, R.2
  • 37
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucl Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.1    Madden, T.2    Schaffer, A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.7
  • 38
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden markov models that represent all proteins of known structure
    • Gough J, Karplus K, Hughey R, Chothia C. Assignment of homology to genome sequences using a library of hidden markov models that represent all proteins of known structure. Molecular Biology 2001, 313(4):903-919.
    • (2001) Molecular Biology , vol.313 , Issue.4 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 39
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan - an integration platform for the signature-recognition methods in InterPro
    • 10.1093/bioinformatics/17.9.847, 11590104
    • Zdobnov E, Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17(9):847-848. 10.1093/bioinformatics/17.9.847, 11590104.
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 847-848
    • Zdobnov, E.1    Apweiler, R.2
  • 42
    • 0004140497 scopus 로고    scopus 로고
    • Out-of-bag estimation
    • Technical Report, Statistics Department, University of California
    • Breiman L. Out-of-bag estimation. 1996, Technical Report, Statistics Department, University of California., http://ftp.stat.berkeley.edu/pub/users/breiman/OOBestimation.ps.Z
    • (1996)
    • Breiman, L.1
  • 43
    • 0001884644 scopus 로고
    • Individual comparisons by ranking methods
    • Wilcoxon F. Individual comparisons by ranking methods. Biometrics 1945, 1:80-83.
    • (1945) Biometrics , vol.1 , pp. 80-83
    • Wilcoxon, F.1
  • 44
    • 0002714543 scopus 로고    scopus 로고
    • Making large-scale SVM learning practical
    • MIT-Press, Cambridge, MA, USA, Scholkopf B, Burges C, Smola A
    • Joachims T. Making large-scale SVM learning practical. Advances in Kernel Methods - Support Vector Learning 1999, MIT-Press, Cambridge, MA, USA, Scholkopf B, Burges C, Smola A.
    • (1999) Advances in Kernel Methods - Support Vector Learning
    • Joachims, T.1


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