메뉴 건너뛰기




Volumn 9, Issue 2, 2012, Pages 609-618

Subcellular localization prediction through boosting association rules

Author keywords

bioinformatics (genome or protein) databases; Clustering classification and association rules; pattern recognition

Indexed keywords

AMINO ACID COMPOSITIONS; BENCHMARK DATA; BIOINFORMATICS (GENOME OR PROTEIN) DATABASE; BOOSTING ALGORITHM; C-TERMINUS; CLASSIFICATION PERFORMANCE; DOCUMENT CLASSIFICATION; N-TERMINALS; ONLINE PREDICTION; PROTEIN DATABASE; PROTEIN SEQUENCES; PROTEIN SUBCELLULAR LOCALIZATION; SORTING SIGNALS; SUBCELLULAR LOCALIZATIONS; SUBCELLULAR LOCATION; TEST COVERAGE; TEXT ANNOTATIONS;

EID: 84856466037     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.131     Document Type: Article
Times cited : (22)

References (39)
  • 1
    • 0031887946 scopus 로고    scopus 로고
    • Wanted: Subcellular localization of proteins based on sequence
    • DOI 10.1016/S0962-8924(98)01226-4, PII S0962892498012264
    • B. Eisenhaber and P. Bork, "Wanted: Subcellular Localization of Proteins Based on Sequence," Trends in Cell Biology, vol. 9, pp. 169-170, 1998. (Pubitemid 28142265)
    • (1998) Trends in Cell Biology , vol.8 , Issue.4 , pp. 169-170
    • Eisenhaber, F.1    Bork, P.2
  • 2
    • 0029979607 scopus 로고    scopus 로고
    • Common principles of protein translocation across membranes
    • G. Schatz and B. Dobberstein, "Common Principles of Protein Translocation across Membranes," Science, vol. 271, no. 5255, pp. 1519-1526, 1996. (Pubitemid 26097210)
    • (1996) Science , vol.271 , Issue.5255 , pp. 1519-1526
    • Schatz, G.1    Dobberstein, B.2
  • 3
    • 0033909566 scopus 로고    scopus 로고
    • Protein sorting signals and prediction of subcellular localization
    • K. Nakai, "Protein Sorting Signals and Prediction of Subcellular Localization," Advances in Protein Chemistry, vol. 54, pp. 277-344, 2000. (Pubitemid 30458951)
    • (2000) Advances in Protein Chemistry , vol.54 , pp. 277-344
    • Nakai, K.1
  • 4
    • 0027105007 scopus 로고
    • A knowledge base for predicting protein localization sites in eukaryotic cells
    • DOI 10.1016/S0888-7543(05)80111-9
    • K. Nakai and M. Kanehisa, "A Knowledge Base for Predicting Protein Localization Sites in Eukaryotic Cells," Genomics, vol. 14, pp. 897-911, 1992. (Pubitemid 23053027)
    • (1992) Genomics , vol.14 , Issue.4 , pp. 897-911
    • Nakai, K.1    Kanehisa, M.2
  • 5
    • 0034697980 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins based on their n-terminal amino acid sequence
    • O. Emanuelsson, H. Nielsen, S. Brunak, and G. von Heijne, "Predicting Subcellular Localization of Proteins Based on Their n-Terminal Amino Acid Sequence," J. Molecular Biology, vol. 300, pp. 1005-1016, 2000.
    • (2000) J. Molecular Biology , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    Von Heijne, G.4
  • 6
    • 0036187913 scopus 로고    scopus 로고
    • Extensive feature detection of N-terminal protein sorting signals
    • H. Bannai, Y. Tamada, O. Maruyama, K. Nakai, and S. Miyano, "Extensive Feature Detection of N-Terminal Protein Sorting Signals," Bioinformatics, vol. 18, no. 2, pp. 298-305, 2002. (Pubitemid 34183107)
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 298-305
    • Bannai, H.1    Tamada, Y.2    Maruyama, O.3    Nakai, K.4    Miyano, S.5
  • 7
    • 0141515750 scopus 로고    scopus 로고
    • Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino pairs
    • DOI 10.1093/bioinformatics/btg222
    • K.-J. Park and M. Kanehisa, "Prediction of Protein Subcellular Locations by Support Vector Machines Using Compositions of Amino Acids and Amino Acid Pairs," Bioinformatics, vol. 19, no. 13, pp. 1656-1663, 2003. (Pubitemid 37121154)
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1656-1663
    • Park, K.-J.1    Kanehisa, M.2
  • 8
    • 2442671554 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins in a hybridization space
    • DOI 10.1093/bioinformatics/bth054
    • Y.-D. Cai and K.-C. Chou, "Predicting Subcellular Localization of Proteins in a Hybridization Space," Bioinformatics, vol. 20, no. 7, pp. 1151-1156, 2004. (Pubitemid 38660352)
    • (2004) Bioinformatics , vol.20 , Issue.7 , pp. 1151-1156
    • Cai, Y.-D.1    Chou, K.-C.2
  • 9
    • 0032940342 scopus 로고    scopus 로고
    • Protein subcellular location prediction
    • K.C. Chou and D.W. Elrod, "Protein Subcellular Location Prediction," Protein Eng., vol. 12, pp. 107-118, 1999. (Pubitemid 29103689)
    • (1999) Protein Engineering , vol.12 , Issue.2 , pp. 107-118
    • Chou, K.-C.1    Elrod, D.W.2
  • 10
    • 2442687039 scopus 로고    scopus 로고
    • Combining text mining and sequence analysis to discover protein functional regions
    • E. Eskin and E. Agichtein, "Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions," Proc. Pacific Symp. Biocomputing, pp. 288-299, 2004.
    • (2004) Proc. Pacific Symp. Biocomputing , pp. 288-299
    • Eskin, E.1    Agichtein, E.2
  • 11
    • 34248205175 scopus 로고    scopus 로고
    • Predicting nuclear localization
    • DOI 10.1021/pr060564n
    • J. Hawkins, L. Davis, and M. Boden, "Predicting Nuclear Localization," J. Proteome Research, vol. 6, pp. 1402-1409, 2007. (Pubitemid 46724037)
    • (2007) Journal of Proteome Research , vol.6 , Issue.4 , pp. 1402-1409
    • Hawkins, J.1    Davis, L.2    Boden, M.3
  • 12
    • 0344480548 scopus 로고    scopus 로고
    • Inferring sub-cellular localization through automated lexical analysis
    • R. Nair and B. Rost, "Inferring Sub-Cellular Localization through Automated Lexical Analysis," Bioinformatics, vol. 28, pp. S78-S86, 2002. (Pubitemid 41185640)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Nair, R.1    Rost, B.2
  • 13
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • A. Bairoch and R. Apweiler, "The Swiss-Prot Protein Sequence Database and Its Supplement Trembl in 2000," Nucleic Acids Research, vol. 28, no. 1, pp. 45-48, 2000. (Pubitemid 30047711)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 14
    • 1542400030 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins using machine-learned classifiers
    • DOI 10.1093/bioinformatics/btg447
    • Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner, "Predicting Subcellular Localization of Proteins Using Machine-Learned Classifiers," Bioinformatics, vol. 20, no. 4, pp. 547-556, 2004. (Pubitemid 38344335)
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 547-556
    • Lu, Z.1    Szafron, D.2    Greiner, R.3    Lu, P.4    Wishart, D.S.5    Poulin, B.6    Anvik, J.7    Macdonell, C.8    Eisner, R.9
  • 15
    • 33646861792 scopus 로고    scopus 로고
    • MultiLoc: Prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
    • DOI 10.1093/bioinformatics/btl002
    • A. Höglund, P. Dönnes, T. Blum, H.-W. Adolph, and O. Kohlbacher, "Multiloc: Prediction of Protein Subcellular Localization Using N-Terminal Targeting Sequences, Sequence Motifs and Amino Acid Composition," Bioinformatics, vol. 22, no. 10, pp. 1158-1165, 2006. (Pubitemid 43779005)
    • (2006) Bioinformatics , vol.22 , Issue.10 , pp. 1158-1165
    • Hoglund, A.1    Donnes, P.2    Blum, T.3    Adolph, H.-W.4    Kohlbacher, O.5
  • 16
    • 0037249644 scopus 로고    scopus 로고
    • NLSdb: Database of nuclear localization signals
    • DOI 10.1093/nar/gkg001
    • R. Nair, P. Carter, and B. Rost, "NLSdb: Database of Nuclear Localization Signals," Nucleic Acids Research, vol. 31, pp. 397-399, 2003. (Pubitemid 36150411)
    • (2003) Nucleic Acids Research , vol.31 , Issue.1 , pp. 397-399
    • Nair, R.1    Carter, P.2    Rost, B.3
  • 17
    • 0028111863 scopus 로고
    • PROSITE: Recent developments
    • A. Bairoch and P. Bucher, "Prosite: Recent Developments," Nucleic Acids Research, vol. 22, pp. 3583-3589, 1994. (Pubitemid 24299830)
    • (1994) Nucleic Acids Research , vol.22 , Issue.17 , pp. 3583-3589
    • Bairoch, A.1    Bucher, P.2
  • 18
    • 34447304880 scopus 로고    scopus 로고
    • SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
    • DOI 10.1093/bioinformatics/btm115
    • H. Shatkay, A. Höglund, S. Brady, T. Blum, P. Dönnes, and O. Kohlbacher, "Sherloc: High-Accuracy Prediction of Protein Localization by Integrating Text and Protein Sequence Data," Bioinformatics, vol. 23, no. 11, pp. 1410-1417, 2007. (Pubitemid 47050524)
    • (2007) Bioinformatics , vol.23 , Issue.11 , pp. 1410-1417
    • Shatkay, H.1    Hoglund, A.2    Brady, S.3    Blum, T.4    Donnes, P.5    Kohlbacher, O.6
  • 19
    • 33745759451 scopus 로고    scopus 로고
    • Hum-PLoc: A novel ensemble classifier for predicting human protein subcellular localization
    • DOI 10.1016/j.bbrc.2006.06.059, PII S0006291X06013593
    • K.-C. Chou and H.-B. Shen, "Hum-PLoc: A Novel Ensemble Classifier for Predicting Human Protein Subcellular Localization," Biochemical and Biophisical Research Comm., vol. 347, pp. 150-157, 2006. (Pubitemid 44015660)
    • (2006) Biochemical and Biophysical Research Communications , vol.347 , Issue.1 , pp. 150-157
    • Chou, K.-C.1    Shen, H.-B.2
  • 20
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • DOI 10.1016/j.ab.2007.07.006, PII S0003269707004423
    • K.-C. Chou and H.-B. Shen, "Review: Recent Progresses in Protein Subcellular Location Prediction," Analytical Biochemistry, vol. 370, pp. 1-16, 2007. (Pubitemid 47404494)
    • (2007) Analytical Biochemistry , vol.370 , Issue.1 , pp. 1-16
    • Chou, K.-C.1    Shen, H.-B.2
  • 23
    • 41449117926 scopus 로고    scopus 로고
    • Predicting subcellular localization with AdaBoost learner
    • DOI 10.2174/092986608783744234
    • Y. Jin, B. Niu, K. Feng, W. Lu, Y. Cai, and G. Li, "Predicting Subcellular Localization with Adaboost Learner," Protein and Peptide Letters, vol. 15, no. 1, pp. 286-289, 2008. (Pubitemid 351457378)
    • (2008) Protein and Peptide Letters , vol.15 , Issue.3 , pp. 286-289
    • Jin, Y.-H.1    Niu, B.2    Feng, K.-Y.3    Lu, W.-C.4    Cai, Y.-D.5    Li, G.-Z.6
  • 28
    • 78149313084 scopus 로고    scopus 로고
    • CMAR: Accurate and efficient classification based on multiple class-association rules
    • W. Li, J. Han, and J. Pei, "CMAR: Accurate and Efficient Classification Based on Multiple Class-Association Rules," Proc. IEEE Int'l Conf. Data Mining (ICDM), pp. 369-376, 2001.
    • (2001) Proc. IEEE Int'l Conf. Data Mining (ICDM) , pp. 369-376
    • Li, W.1    Han, J.2    Pei, J.3
  • 30
    • 39449105071 scopus 로고    scopus 로고
    • Cell-PLoc: A package of web servers for predicting subcellular localization of proteins in various organisms
    • K.C. Chou and H.B. Shen, "Cell-PLoc: A Package of Web Servers for Predicting Subcellular Localization of Proteins in Various Organisms," Nature Protocols, vol. 3, no. 2, pp. 153-162, http:// dx.doi.org/10.1038/nprot. 2007.494, 2008.
    • (2008) Nature Protocols , vol.3 , Issue.2 , pp. 153-162
    • Chou, K.C.1    Shen, H.B.2
  • 31
    • 0025448521 scopus 로고
    • The strength of weak learnability
    • R.E. Schapire, "The Strength of Weak Learnability," Machine Learning, vol. 5, pp. 197-227, citeseer.ist.psu.edu/schapire90 strength.html, 1990.
    • (1990) Machine Learning , vol.5 , pp. 197-227
    • Schapire, R.E.1
  • 32
    • 0031211090 scopus 로고    scopus 로고
    • A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting
    • Y. Freund and R.E. Schapire, "A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting," J. Computer and System Sciences, vol. 55, no. 1, pp. 119-139, 1997. (Pubitemid 127433398)
    • (1997) Journal of Computer and System Sciences , vol.55 , Issue.1 , pp. 119-139
    • Freund, Y.1    Schapire, R.E.2
  • 34
    • 34548439881 scopus 로고    scopus 로고
    • Using chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes
    • C.C.L.Z.C. Zhou, X.B., and X.Y. Zou, "Using Chou's Amphiphilic Pseudo-Amino Acid Composition and Support Vector Machine for Prediction of Enzyme Subfamily Classes," J. Theoretical Biology, vol. 248, pp. 546-551, 2007.
    • (2007) J. Theoretical Biology , vol.248 , pp. 546-551
    • Zhou, C.C.L.Z.C.X.B.1    Zou, X.Y.2
  • 35
    • 70349613231 scopus 로고    scopus 로고
    • Foldrate: A web-server for predicting protein folding rates from primary sequence
    • K.C. Chou and H.B. Shen, "Foldrate: A Web-Server for Predicting Protein Folding Rates from Primary Sequence," The Open Bioinformatics J., vol. 3, pp. 31-50, 2009.
    • (2009) The Open Bioinformatics J. , vol.3 , pp. 31-50
    • Chou, K.C.1    Shen, H.B.2
  • 38
    • 85053374465 scopus 로고    scopus 로고
    • Making use of the most expressive jumping emerging patterns for classification
    • J. Li, G. Dong, and K. Ramamohanarao, "Making Use of the Most Expressive Jumping Emerging Patterns for Classification," Knowledge and Information Systems, vol. 3, no. 2, pp. 131-145, 2001.
    • (2001) Knowledge and Information Systems , vol.3 , Issue.2 , pp. 131-145
    • Li, J.1    Dong, G.2    Ramamohanarao, K.3
  • 39
    • 60849112567 scopus 로고    scopus 로고
    • A new classification method using array comparative genome hybridization data, based on the concept of limited jumping emerging patterns
    • article S64
    • T. Gambin and K. Walczak, "A New Classification Method Using Array Comparative Genome Hybridization Data, Based on the Concept of Limited Jumping Emerging Patterns," BMC Bioinformatics, vol. 10(Suppl 1), article S64, 2009.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 1
    • Gambin, T.1    Walczak, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.