메뉴 건너뛰기




Volumn 14, Issue 4, 2010, Pages 815-819

A knowledge-based method to predict the cooperative relationship between transcription factors

Author keywords

Amino acid composition; BLAST; Functional domain composition; Jackknife cross validation test; The nearest neighbor algorithm; Transcription factor cooperation

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 78650178423     PISSN: 13811991     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11030-009-9177-1     Document Type: Article
Times cited : (4)

References (31)
  • 1
    • 0035971496 scopus 로고    scopus 로고
    • Distinct roles of Jun:Fos and Jun:ATF dimers in oncogenesis
    • DOI 10.1038/sj.onc.1204239
    • H van Dam M Castellazzi 2001 Distinct roles of Jun: Fos and Jun: ATF dimers in oncogenesis Oncogene 20 2453 2464 10.1038/sj.onc.1204239 10.1038/sj.onc.1204239 11402340 (Pubitemid 32531302)
    • (2001) Oncogene , vol.20 , Issue.19 REV. ISSUE 2 , pp. 2453-2464
    • Van Dam, H.1    Castellazzi, M.2
  • 2
    • 0025276217 scopus 로고
    • Heterodimer formation between CREB and JUN proteins
    • 1:CAS:528:DyaK3cXktVaitrY%3D 2138276
    • DM Benbrook NC Jones 1990 Heterodimer formation between CREB and JUN proteins Oncogene 5 295 302 1:CAS:528:DyaK3cXktVaitrY%3D 2138276
    • (1990) Oncogene , vol.5 , pp. 295-302
    • Benbrook, D.M.1    Jones, N.C.2
  • 3
    • 0025239414 scopus 로고
    • MXBP/CRE-BP2 and c-Jun form a complex which binds to the cyclic AMP, but not to the 12-O-tetradecanoylphorbol-13-acetate, response element
    • 1:CAS:528:DyaK3cXhslemsLs%3D 2138707
    • LB Ivashkiv, et al. 1990 mXBP/CRE-BP2 and c-Jun form a complex which binds to the cyclic AMP, but not to the 12-O-tetradecanoylphorbol-13-acetate, response element Mol Cell Biol 10 1609 1621 1:CAS:528:DyaK3cXhslemsLs%3D 2138707
    • (1990) Mol Cell Biol , vol.10 , pp. 1609-1621
    • Ivashkiv, L.B.1
  • 4
    • 0029328342 scopus 로고
    • Transcriptional control by protein phosphorylation: Signal transmission from the cell surface to the nucleus
    • 10.1016/S0960-9822 1:CAS:528:DyaK2MXnt1agsrc%3D 10.1016/S0960-9822(95) 00151-5 7583121
    • M Karin T Hunter 1995 Transcriptional control by protein phosphorylation: signal transmission from the cell surface to the nucleus Curr Biol 5 747 757 10.1016/S0960-9822 1:CAS:528:DyaK2MXnt1agsrc%3D 10.1016/S0960-9822(95)00151-5 7583121
    • (1995) Curr Biol , vol.5 , pp. 747-757
    • Karin, M.1    Hunter, T.2
  • 5
    • 0030906497 scopus 로고    scopus 로고
    • AP-1 function and regulation
    • 10.1016/S0955-0674 1:CAS:528:DyaK2sXisVWlsL0%3D 10.1016/S0955-0674(97) 80068-3 9069263
    • M Karin Z Liu E Zandi 1997 AP-1 function and regulation Curr Opin Cell Biol 9 240 246 10.1016/S0955-0674 1:CAS:528:DyaK2sXisVWlsL0%3D 10.1016/S0955-0674(97)80068-3 9069263
    • (1997) Curr Opin Cell Biol , vol.9 , pp. 240-246
    • Karin, M.1    Liu, Z.2    Zandi, E.3
  • 6
    • 0031723586 scopus 로고    scopus 로고
    • Transcription factor ATF2 cooperates with v-Jun to promote growth factor-independent proliferation in vitro and tumor formation in vivo
    • 1:CAS:528:DyaK1cXnvVKltL8%3D 9819389
    • S Huguier, et al. 1998 Transcription factor ATF2 cooperates with v-Jun to promote growth factor-independent proliferation in vitro and tumor formation in vivo Mol Cell Biol 18 7020 7029 1:CAS:528:DyaK1cXnvVKltL8%3D 9819389
    • (1998) Mol Cell Biol , vol.18 , pp. 7020-7029
    • Huguier, S.1
  • 7
    • 65449116159 scopus 로고    scopus 로고
    • Opposing roles for ATF2 and c-Fos in c-Jun-mediated neuronal apoptosis
    • 10.1128/MCB.01344-08 1:CAS:528:DC%2BD1MXlt1Orurw%3D 10.1128/MCB.01344-08 19255142
    • Z Yuan, et al. 2009 Opposing roles for ATF2 and c-Fos in c-Jun-mediated neuronal apoptosis Mol Cell Biol 29 2431 2442 10.1128/MCB.01344-08 1:CAS:528:DC%2BD1MXlt1Orurw%3D 10.1128/MCB.01344-08 19255142
    • (2009) Mol Cell Biol , vol.29 , pp. 2431-2442
    • Yuan, Z.1
  • 8
    • 0036375851 scopus 로고    scopus 로고
    • Transcriptional activation of C/EBPbeta gene by c-Jun and ATF2
    • 1:CAS:528:DC%2BD38Xmtl2gur0%3D 10.1089/104454902320308924 12215258
    • WC Lin, et al. 2002 Transcriptional activation of C/EBPbeta gene by c-Jun and ATF2 DNA Cell Biol 21 551 560 1:CAS:528:DC%2BD38Xmtl2gur0%3D 10.1089/104454902320308924 12215258
    • (2002) DNA Cell Biol , vol.21 , pp. 551-560
    • Lin, W.C.1
  • 9
    • 13544254744 scopus 로고    scopus 로고
    • Identifying combinatorial regulation of transcription factors and binding motifs
    • 10.1186/gb-2004-5-8-r56 10.1186/gb-2004-5-8-r56 15287978
    • M Kato, et al. 2004 Identifying combinatorial regulation of transcription factors and binding motifs Genome Biol 5 R56 10.1186/gb-2004-5-8-r56 10.1186/gb-2004-5-8-r56 15287978
    • (2004) Genome Biol , vol.5 , pp. 56
    • Kato, M.1
  • 10
    • 24144495286 scopus 로고    scopus 로고
    • Identifying cooperative transcriptional regulations using protein-protein interactions
    • DOI 10.1093/nar/gki793
    • N Nagamine Y Kawada Y Sakakibara 2005 Identifying cooperative transcriptional regulations using protein-protein interactions Nucleic Acids Res 33 4828 4837 10.1093/nar/gki793 1:CAS:528:DC%2BD2MXpvFKjtL4%3D 10.1093/nar/gki793 16126847 (Pubitemid 41418882)
    • (2005) Nucleic Acids Research , vol.33 , Issue.15 , pp. 4828-4837
    • Nagamine, N.1    Kawada, Y.2    Sakakibara, Y.3
  • 11
    • 33644855121 scopus 로고    scopus 로고
    • Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae
    • DOI 10.1093/nar/gkj487
    • X Yu, et al. 2006 Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae Nucleic Acids Res 34 917 927 10.1093/nar/gkj487 1:CAS:528:DC%2BD28Xhs1Sktbc%3D 10.1093/nar/gkj487 16464824 (Pubitemid 43380675)
    • (2006) Nucleic Acids Research , vol.34 , Issue.3 , pp. 917-927
    • Yu, X.1    Lin, J.2    Masuda, T.3    Esumi, N.4    Zack, D.J.5    Qian, J.6
  • 12
    • 14844285429 scopus 로고    scopus 로고
    • Using functional domain composition to predict enzyme family classes
    • DOI 10.1021/pr049835p
    • YD Cai KC Chou 2005 Using functional domain composition to predict enzyme family classes J Proteome Res 4 109 111 10.1021/pr049835p 1:CAS:528: DC%2BD2cXhtFWqsr%2FJ 10.1021/pr049835p 15707365 (Pubitemid 40344463)
    • (2005) Journal of Proteome Research , vol.4 , Issue.1 , pp. 109-111
    • Cai, Y.-D.1    Chou, K.-C.2
  • 13
    • 33745752255 scopus 로고    scopus 로고
    • Automatic transcription factor classifier based on functional domain composition
    • DOI 10.1016/j.bbrc.2006.06.060, PII S0006291X0601357X
    • Z Qian YD Cai YX Li 2006 Automatic transcription factor classifier based on functional domain composition Biochem Biophys Res Commun 347 141 144 10.1016/j.bbrc.2006.06.060 1:CAS:528:DC%2BD28Xmslyrsbk%3D 10.1016/j.bbrc.2006. 06.060 16808896 (Pubitemid 44015658)
    • (2006) Biochemical and Biophysical Research Communications , vol.347 , Issue.1 , pp. 141-144
    • Qian, Z.1    Cai, Y.-D.2    Li, Y.3
  • 14
    • 0000515372 scopus 로고    scopus 로고
    • InterPro: An integrated documentation resource for protein families, domains and functional sites
    • 10.1093/bib/3.3.225 1:CAS:528:DC%2BD38XnsFOhtbs%3D 10.1093/bib/3.3.225 12230031
    • NJ Mulder, et al. 2002 InterPro: an integrated documentation resource for protein families, domains and functional sites Brief Bioinform 3 225 235 10.1093/bib/3.3.225 1:CAS:528:DC%2BD38XnsFOhtbs%3D 10.1093/bib/3.3.225 12230031
    • (2002) Brief Bioinform , vol.3 , pp. 225-235
    • Mulder, N.J.1
  • 15
    • 4544322645 scopus 로고    scopus 로고
    • Predicting 22 protein localizations in budding yeast
    • DOI 10.1016/j.bbrc.2004.08.113, PII S0006291X04018315
    • YD Cai KC Chou 2004 Predicting 22 protein localizations in budding yeast Biochem Biophys Res Commun 323 425 428 10.1016/j.bbrc.2004.08.113 1:CAS:528:DC%2BD2cXnsVyqtr4%3D 10.1016/j.bbrc.2004.08.113 15369769 (Pubitemid 39221115)
    • (2004) Biochemical and Biophysical Research Communications , vol.323 , Issue.2 , pp. 425-428
    • Cai, Y.-D.1    Chou, K.-C.2
  • 16
    • 32344433486 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from sequences in a hybridization space
    • DOI 10.1021/pr050331g
    • KC Chou YD Cai 2006 Predicting protein-protein interactions from sequences in a hybridization space J Proteome Res 5 316 322 10.1021/pr050331g 1:CAS:528:DC%2BD2MXhtlClsLnK 10.1021/pr050331g 16457597 (Pubitemid 43222299)
    • (2006) Journal of Proteome Research , vol.5 , Issue.2 , pp. 316-322
    • Chou, K.-C.1    Cai, Y.-D.2
  • 17
    • 33747195620 scopus 로고    scopus 로고
    • A novel computational method to predict transcription factor DNA binding preference
    • DOI 10.1016/j.bbrc.2006.07.149, PII S0006291X06017207
    • Z Qian YD Cai YX Li 2006 A novel computational method to predict transcription factor DNA binding preference Biochem Biophys Res Commun 348 1034 1037 10.1016/j.bbrc.2006.07.149 1:CAS:528:DC%2BD28XosVOisrg%3D 10.1016/j.bbrc.2006.07.149 16899225 (Pubitemid 44233519)
    • (2006) Biochemical and Biophysical Research Communications , vol.348 , Issue.3 , pp. 1034-1037
    • Qian, Z.1    Cai, Y.-D.2    Li, Y.3
  • 18
    • 33646180187 scopus 로고    scopus 로고
    • Classification of protein quaternary structure by functional domain composition
    • 10.1186/1471-2105-7-187 10.1186/1471-2105-7-187 16584572
    • X Yu C Wang YX Li 2006 Classification of protein quaternary structure by functional domain composition BMC Bioinformatics 7 187 192 10.1186/1471-2105-7- 187 10.1186/1471-2105-7-187 16584572
    • (2006) BMC Bioinformatics , vol.7 , pp. 187-192
    • Yu, X.1    Wang, C.2    Li, Y.X.3
  • 19
    • 33644876958 scopus 로고    scopus 로고
    • TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
    • 10.1093/nar/gkj143 1:CAS:528:DC%2BD28XisFymtA%3D%3D 10.1093/nar/gkj143 16381825
    • V Matys, et al. 2006 TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucleic Acids Res 34 D108 D110 10.1093/nar/gkj143 1:CAS:528:DC%2BD28XisFymtA%3D%3D 10.1093/nar/gkj143 16381825
    • (2006) Nucleic Acids Res , vol.34
    • Matys, V.1
  • 20
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • DOI 10.1093/nar/24.1.238
    • E Wingender, et al. 1996 TRANSFAC: a database on transcription factors and their DNA binding sites Nucleic Acids Res 24 238 241 1:CAS:528: DyaK28XnsFSiug%3D%3D 10.1093/nar/24.1.238 8594589 (Pubitemid 26085775)
    • (1996) Nucleic Acids Research , vol.24 , Issue.1 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 21
    • 29244482784 scopus 로고    scopus 로고
    • Predicting membrane protein type by functional domain composition and pseudo-amino acid composition
    • DOI 10.1016/j.jtbi.2005.05.035, PII S0022519305002547
    • YD Cai KC Chou 2006 Predicting membrane protein type by functional domain composition and pseudo-amino acid composition J Theor Biol 238 395 400 10.1016/j.jtbi.2005.05.035 1:CAS:528:DC%2BD2MXhtlCrt7vK 10.1016/j.jtbi.2005.05. 035 16040052 (Pubitemid 41828439)
    • (2006) Journal of Theoretical Biology , vol.238 , Issue.2 , pp. 395-400
    • Cai, Y.-D.1    Chou, K.-C.2
  • 22
    • 2442671554 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins in a hybridization space
    • DOI 10.1093/bioinformatics/bth054
    • YD Cai KC Chou 2004 Predicting subcellular localization of proteins in a hybridization space Bioinformatics 20 1151 1156 1:CAS:528:DC%2BD2cXjs1Wrt78%3D 10.1093/bioinformatics/bth054 14764553 (Pubitemid 38660352)
    • (2004) Bioinformatics , vol.20 , Issue.7 , pp. 1151-1156
    • Cai, Y.-D.1    Chou, K.-C.2
  • 23
    • 34248581521 scopus 로고    scopus 로고
    • ECS: An automatic enzyme classifier based on functional domain composition
    • DOI 10.1016/j.compbiolchem.2007.03.008, PII S1476927107000564
    • L Lu, et al. 2007 ECS: an automatic enzyme classifier based on functional domain composition Comput Biol Chem 31 226 332 10.1016/j.compbiolchem.2007.03. 008 1:CAS:528:DC%2BD2sXlvVansL0%3D 10.1016/j.compbiolchem.2007.03.008 17500036 (Pubitemid 46765209)
    • (2007) Computational Biology and Chemistry , vol.31 , Issue.3 , pp. 226-232
    • Lu, L.1    Qian, Z.2    Cai, Y.-D.3    Li, Y.4
  • 24
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • 1:CAS:528:DyaK3MXitVGmsA%3D%3D 2231712
    • SF Altschul, et al. 1990 Basic local alignment search tool J Mol Biol 215 403 410 1:CAS:528:DyaK3MXitVGmsA%3D%3D 2231712
    • (1990) J Mol Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 25
    • 3042621436 scopus 로고    scopus 로고
    • Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition
    • DOI 10.1093/bioinformatics/bth085
    • YD Cai AJ Doig 2004 Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition Bioinformatics 20 1292 1300 1:CAS:528:DC%2BD2cXkt1Srur0%3D 10.1093/bioinformatics/bth085 14976029 (Pubitemid 38811420)
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1292-1300
    • Cai, Y.-D.1    Doig, A.J.2
  • 26
    • 0032534796 scopus 로고    scopus 로고
    • Homology-based gene prediction using neural nets
    • DOI 10.1006/abio.1998.2876
    • YD Cai P Bork 1998 Homology-based gene prediction using neural nets Anal Biochem 265 269 274 10.1006/abio.1998.2876 1:CAS:528:DyaK1MXitVyntw%3D%3D 10.1006/abio.1998.2876 9882402 (Pubitemid 29002071)
    • (1998) Analytical Biochemistry , vol.265 , Issue.2 , pp. 269-274
    • Cai, Y.1    Bork, P.2
  • 27
    • 0042622243 scopus 로고    scopus 로고
    • SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence
    • DOI 10.1093/nar/gkg600
    • CZ Cai, et al. 2003 SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence Nucleic Acids Res 31 3692 3697 1:CAS:528:DC%2BD3sXltVWisrg%3D 10.1093/nar/gkg600 12824396 (Pubitemid 37442225)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3692-3697
    • Cai, C.Z.1    Han, L.Y.2    Ji, Z.L.3    Chen, X.4    Chen, Y.Z.5
  • 28
    • 0038705861 scopus 로고    scopus 로고
    • Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition
    • DOI 10.1016/S0006-291X(03)00775-7
    • YD Cai KC Chou 2003 Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition Biochem Biophys Res Commun 305 407 411 10.1016/S0006-291X(03) 00775-7 1:CAS:528:DC%2BD3sXjs1erurg%3D 10.1016/S0006-291X(03)00775-7 12745090 (Pubitemid 36555484)
    • (2003) Biochemical and Biophysical Research Communications , vol.305 , Issue.2 , pp. 407-411
    • Cai, Y.-D.1    Chou, K.-C.2
  • 29
    • 14844285429 scopus 로고    scopus 로고
    • Using functional domain composition to predict enzyme family classes
    • DOI 10.1021/pr049835p
    • YD Cai KC Chou 2005 Using functional domain composition to predict enzyme family classes J Proteome Res 4 109 111 10.1021/pr049835p 1:CAS:528: DC%2BD2cXhtFWqsr%2FJ 10.1021/pr049835p 15707365 (Pubitemid 40344463)
    • (2005) Journal of Proteome Research , vol.4 , Issue.1 , pp. 109-111
    • Cai, Y.-D.1    Chou, K.-C.2
  • 31
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan-an integration platform for the signature-recognition methods in InterPro
    • 1:CAS:528:DC%2BD3MXotFehsro%3D 10.1093/bioinformatics/17.9.847 11590104
    • EM Zdobnov R Apweiler 2001 InterProScan-an integration platform for the signature-recognition methods in InterPro Bioinformatics 17 847 848 1:CAS:528:DC%2BD3MXotFehsro%3D 10.1093/bioinformatics/17.9.847 11590104
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.