메뉴 건너뛰기




Volumn 8, Issue 9, 2007, Pages

Cross-species cluster co-conservation: A new method for generating protein interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

EID: 38349087432     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-9-r185     Document Type: Article
Times cited : (10)

References (39)
  • 1
    • 0033551248 scopus 로고    scopus 로고
    • Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
    • 16324 10200254 10.1073/pnas.96.8.4285
    • Pellegrini M Marcotte EM Thompson MJ Eisenberg D Yeates TO Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96:4285-4288. 16324 10200254 10.1073/pnas.96.8.4285
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 4285-4288
    • Pellegrini, M.1    Marcotte, E.M.2    Thompson, M.J.3    Eisenberg, D.4    Yeates, T.O.5
  • 2
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • 10.1126/science.285.5428.751 10427000
    • Marcotte EM Pellegrini M Ng HL Rice DW Yeates TO Eisenberg D Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285:751-753. 10.1126/science.285.5428.751 10427000
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 3
    • 0347824672 scopus 로고    scopus 로고
    • Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach
    • 193659 12952538 10.1186/gb-2003-4-9-r59
    • Strong M Mallick P Pellegrini M Thompson MJ Eisenberg D Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach. Genome Biol 2003, 4:R59. 193659 12952538 10.1186/ gb-2003-4-9-r59
    • (2003) Genome Biol , vol.4
    • Strong, M.1    Mallick, P.2    Pellegrini, M.3    Thompson, M.J.4    Eisenberg, D.5
  • 4
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
    • 310926 10958638 10.1101/gr.10.8.1204
    • Huynen M Snel B Lathe W 3rd Bork P Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res 2000, 10:1204-1210. 310926 10958638 10.1101/gr.10.8.1204
    • (2000) Genome Res , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe III, W.3    Bork, P.4
  • 5
    • 0036081482 scopus 로고    scopus 로고
    • Predictome: A database of putative functional links between proteins
    • 99135 11752322 10.1093/nar/30.1.306
    • Mellor JC Yanai I Clodfelter KH Mintseris J DeLisi C Predictome: A database of putative functional links between proteins. Nucleic Acids Res 2002, 30:306-309. 99135 11752322 10.1093/nar/30.1.306
    • (2002) Nucleic Acids Res , vol.30 , pp. 306-309
    • Mellor, J.C.1    Yanai, I.2    Clodfelter, K.H.3    Mintseris, J.4    DeLisi, C.5
  • 6
    • 4644231028 scopus 로고    scopus 로고
    • Prolinks: A database of protein functional linkages derived from coevolution
    • 416471 15128449 10.1186/gb-2004-5-5-r35
    • Bowers PM Pellegrini M Thompson MJ Fierro J Yeates TO Eisenberg D Prolinks: A database of protein functional linkages derived from coevolution. Genome Biol 2004, 5:R35. 416471 15128449 10.1186/ gb-2004-5-5-r35
    • (2004) Genome Biol , vol.5
    • Bowers, P.M.1    Pellegrini, M.2    Thompson, M.J.3    Fierro, J.4    Yeates, T.O.5    Eisenberg, D.6
  • 7
    • 19544393944 scopus 로고    scopus 로고
    • Protein function prediction using the Protein Link EXplorer (PLEX)
    • 10.1093/bioinformatics/bti313 15701682
    • Date SV Marcotte EM Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics 2005, 21:2558-2559. 10.1093/ bioinformatics/bti313 15701682
    • (2005) Bioinformatics , vol.21 , pp. 2558-2559
    • Date, S.V.1    Marcotte, E.M.2
  • 8
    • 0037250152 scopus 로고    scopus 로고
    • STRING: A database of predicted functional associations between proteins
    • 165481 12519996 10.1093/nar/gkg034
    • von Mering C Huynen M Jaeggi D Schmidt S Bork P Snel B STRING: A database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31:258-261. 165481 12519996 10.1093/nar/gkg034
    • (2003) Nucleic Acids Res , vol.31 , pp. 258-261
    • von Mering, C.1    Huynen, M.2    Jaeggi, D.3    Schmidt, S.4    Bork, P.5    Snel, B.6
  • 9
    • 0037057376 scopus 로고    scopus 로고
    • Genomic functional annotation using co-evolution profiles of gene clusters
    • 133444 12429059 10.1186/gb-2002-3-11-research0060
    • Zheng Y Roberts RJ Kasif S Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol 2002, 3:RESEARCH0060. 133444 12429059 10.1186/gb-2002-3-11-research0060
    • (2002) Genome Biol , vol.3
    • Zheng, Y.1    Roberts, R.J.2    Kasif, S.3
  • 10
    • 9244239761 scopus 로고    scopus 로고
    • A domain interaction map based on phylogenetic profiling
    • 10.1016/j.jmb.2004.10.019 15561146
    • Pagel P Wong P Frishman D A domain interaction map based on phylogenetic profiling. J Mol Biol 2004, 344:1331-1346. 10.1016/j.jmb.2004.10.019 15561146
    • (2004) J Mol Biol , vol.344 , pp. 1331-1346
    • Pagel, P.1    Wong, P.2    Frishman, D.3
  • 11
    • 55449127787 scopus 로고    scopus 로고
    • Predicting functional gene links from phylogenetic-statistical analyses of whole genomes
    • 1183509 16103904 10.1371/journal.pcbi.0010003
    • Barker D Pagel M Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol 2005, 1:e3. 1183509 16103904 10.1371/journal.pcbi.0010003
    • (2005) PLoS Comput Biol , vol.1
    • Barker, D.1    Pagel, M.2
  • 12
    • 0030046503 scopus 로고    scopus 로고
    • Escherichia coli fliAZY operon
    • 177617 8550423
    • Mytelka DS Chamberlin MJ Escherichia coli fliAZY operon. J Bacteriol 1996, 178:24-34. 177617 8550423
    • (1996) J Bacteriol , vol.178 , pp. 24-34
    • Mytelka, D.S.1    Chamberlin, M.J.2
  • 13
    • 0028165834 scopus 로고
    • Effect of motility on surface colonization and reproductive success of Pseudomonas fluorescens in dual-dilution continuous culture and batch culture systems
    • 201498 16349247
    • Korber DR Lawrence JR Caldwell DE Effect of motility on surface colonization and reproductive success of Pseudomonas fluorescens in dual-dilution continuous culture and batch culture systems. Appl Environ Microbiol 1994, 60:1421-1429. 201498 16349247
    • (1994) Appl Environ Microbiol , vol.60 , pp. 1421-1429
    • Korber, D.R.1    Lawrence, J.R.2    Caldwell, D.E.3
  • 14
    • 0031754332 scopus 로고    scopus 로고
    • Genetic analysis of Escherichia coli biofilm formation: Roles of flagella, motility, chemotaxis and type I pili
    • 10.1046/j.1365-2958.1998.01061.x 9791174
    • Pratt LA Kolter R Genetic analysis of Escherichia coli biofilm formation: Roles of flagella, motility, chemotaxis and type I pili. Mol Microbiol 1998, 30:285-293. 10.1046/j.1365-2958.1998.01061.x 9791174
    • (1998) Mol Microbiol , vol.30 , pp. 285-293
    • Pratt, L.A.1    Kolter, R.2
  • 15
    • 0031951329 scopus 로고    scopus 로고
    • Bacterial locomotion and signal transduction
    • 106986 9495737
    • Manson MD Armitage JP Hoch JA Macnab RM Bacterial locomotion and signal transduction. J Bacteriol 1998, 180:1009-1022. 106986 9495737
    • (1998) J Bacteriol , vol.180 , pp. 1009-1022
    • Manson, M.D.1    Armitage, J.P.2    Hoch, J.A.3    Macnab, R.M.4
  • 16
    • 0033591446 scopus 로고    scopus 로고
    • Type III secretion machines: Bacterial devices for protein delivery into host cells
    • 10.1126/science.284.5418.1322 10334981
    • Galan JE Collmer A Type III secretion machines: Bacterial devices for protein delivery into host cells. Science 1999, 284:1322-1328. 10.1126/ science.284.5418.1322 10334981
    • (1999) Science , vol.284 , pp. 1322-1328
    • Galan, J.E.1    Collmer, A.2
  • 17
    • 0030253637 scopus 로고    scopus 로고
    • Molecular mechanisms of bacterial virulence: Type III secretion and pathogenicity islands
    • 8969244
    • Mecsas JJ Strauss EJ Molecular mechanisms of bacterial virulence: Type III secretion and pathogenicity islands. Emerg Infect Dis 1996, 2:270-288. 8969244
    • (1996) Emerg Infect Dis , vol.2 , pp. 270-288
    • Mecsas, J.J.1    Strauss, E.J.2
  • 18
    • 0034918894 scopus 로고    scopus 로고
    • FlhA, a component of the flagellum assembly apparatus of Pseudomonas aeruginosa, plays a role in internalization by corneal epithelial cells
    • 98584 11447170 10.1128/IAI.69.8.4931-4937.2001
    • Fleiszig SM Arora SK Van R Ramphal R FlhA, a component of the flagellum assembly apparatus of Pseudomonas aeruginosa, plays a role in internalization by corneal epithelial cells. Infect Immun 2001, 69:4931-4937. 98584 11447170 10.1128/IAI.69.8.4931-4937.2001
    • (2001) Infect Immun , vol.69 , pp. 4931-4937
    • Fleiszig, S.M.1    Arora, S.K.2    Van, R.3    Ramphal, R.4
  • 19
    • 4344688129 scopus 로고    scopus 로고
    • GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility
    • 10.1111/j.1365-2958.2004.04206.x 15306016
    • Simm R Morr M Kader A Nimtz M Romling U GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility. Mol Microbiol 2004, 53:1123-1134. 10.1111/j.1365-2958.2004.04206.x 15306016
    • (2004) Mol Microbiol , vol.53 , pp. 1123-1134
    • Simm, R.1    Morr, M.2    Kader, A.3    Nimtz, M.4    Romling, U.5
  • 20
    • 0141484352 scopus 로고    scopus 로고
    • Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose
    • 10.1046/j.1365-2958.2003.03670.x 14507360
    • Spiers AJ Bohannon J Gehrig SM Rainey PB Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Mol Microbiol 2003, 50:15-27. 10.1046/j.1365-2958.2003.03670.x 14507360
    • (2003) Mol Microbiol , vol.50 , pp. 15-27
    • Spiers, A.J.1    Bohannon, J.2    Gehrig, S.M.3    Rainey, P.B.4
  • 21
    • 6044239438 scopus 로고    scopus 로고
    • MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species
    • 523210 15489433 10.1128/JB.186.21.7221-7228.2004
    • Choy WK Zhou L Syn CK Zhang LH Swarup S MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species. J Bacteriol 2004, 186:7221-7228. 523210 15489433 10.1128/JB.186.21.7221-7228.2004
    • (2004) J Bacteriol , vol.186 , pp. 7221-7228
    • Choy, W.K.1    Zhou, L.2    Syn, C.K.3    Zhang, L.H.4    Swarup, S.5
  • 22
    • 0345097587 scopus 로고    scopus 로고
    • FimX, a multidomain protein connecting environmental signals to twitching motility in Pseudomonas aeruginosa
    • 296245 14645265 10.1128/JB.185.24.7068-7076.2003
    • Huang B Whitchurch CB Mattick JS FimX, a multidomain protein connecting environmental signals to twitching motility in Pseudomonas aeruginosa. J Bacteriol 2003, 185:7068-7076. 296245 14645265 10.1128/ JB.185.24.7068-7076.2003
    • (2003) J Bacteriol , vol.185 , pp. 7068-7076
    • Huang, B.1    Whitchurch, C.B.2    Mattick, J.S.3
  • 24
    • 0032484001 scopus 로고    scopus 로고
    • Signal decay through a reverse phosphorelay in the Arc two-component signal transduction system
    • 10.1074/jbc.273.49.32864 9830034
    • Georgellis D Kwon O De Wulf P Lin EC Signal decay through a reverse phosphorelay in the Arc two-component signal transduction system. J Biol Chem 1998, 273:32864-32869. 10.1074/jbc.273.49.32864 9830034
    • (1998) J Biol Chem , vol.273 , pp. 32864-32869
    • Georgellis, D.1    Kwon, O.2    De Wulf, P.3    Lin, E.C.4
  • 25
    • 0142043310 scopus 로고    scopus 로고
    • Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation
    • 10.1016/S0378-1097(03)00507-X 12900028
    • Tenorio E Saeki T Fujita K Kitakawa M Baba T Mori H Isono K Systematic characterization of Escherichia coli genes/ORFs affecting biofilm formation. FEMS Microbiol Lett 2003, 225:107-114. 10.1016/ S0378-1097(03)00507-X 12900028
    • (2003) FEMS Microbiol Lett , vol.225 , pp. 107-114
    • Tenorio, E.1    Saeki, T.2    Fujita, K.3    Kitakawa, M.4    Baba, T.5    Mori, H.6    Isono, K.7
  • 26
    • 10644252538 scopus 로고    scopus 로고
    • Differential gene expression shows natural brominated furanones interfere with the autoinducer-2 bacterial signaling system of Escherichia coli
    • 10.1002/bit.20259 15470704
    • Ren D Bedzyk LA Ye RW Thomas SM Wood TK Differential gene expression shows natural brominated furanones interfere with the autoinducer-2 bacterial signaling system of Escherichia coli. Biotechnol Bioeng 2004, 88:630-642. 10.1002/bit.20259 15470704
    • (2004) Biotechnol Bioeng , vol.88 , pp. 630-642
    • Ren, D.1    Bedzyk, L.A.2    Ye, R.W.3    Thomas, S.M.4    Wood, T.K.5
  • 27
    • 33845948161 scopus 로고    scopus 로고
    • SCALEs: Multiscale analysis of library enrichment
    • 10.1038/nmeth946 17099705
    • Lynch MD Warnecke T Gill RT SCALEs: Multiscale analysis of library enrichment. Nat Methods 2007, 4:87-93. 10.1038/nmeth946 17099705
    • (2007) Nat Methods , vol.4 , pp. 87-93
    • Lynch, M.D.1    Warnecke, T.2    Gill, R.T.3
  • 28
    • 33750029906 scopus 로고    scopus 로고
    • The Rcs phosphorelay system is specific to enteric pathogens/commensals and activates ydeI, a gene important for persistent Salmonella infection of mice
    • 10.1111/j.1365-2958.2006.05420.x 17010160
    • Erickson KD Detweiler CS The Rcs phosphorelay system is specific to enteric pathogens/commensals and activates ydeI, a gene important for persistent Salmonella infection of mice. Mol Microbiol 2006, 62:883-894. 10.1111/j.1365-2958.2006.05420.x 17010160
    • (2006) Mol Microbiol , vol.62 , pp. 883-894
    • Erickson, K.D.1    Detweiler, C.S.2
  • 29
    • 0141430076 scopus 로고    scopus 로고
    • Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events
    • 10.1016/S0378-1119(03)00612-7 12909351
    • Gophna U Ron EZ Graur D Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 2003, 312:151-163. 10.1016/S0378-1119(03)00612-7 12909351
    • (2003) Gene , vol.312 , pp. 151-163
    • Gophna, U.1    Ron, E.Z.2    Graur, D.3
  • 30
    • 0031864184 scopus 로고    scopus 로고
    • Type III protein secretion systems in bacterial pathogens of animals and plants
    • 98920 9618447
    • Hueck CJ Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiol Mol Biol Rev 1998, 62:379-433. 98920 9618447
    • (1998) Microbiol Mol Biol Rev , vol.62 , pp. 379-433
    • Hueck, C.J.1
  • 31
    • 2342565010 scopus 로고    scopus 로고
    • In vitro characterization of FlgB, FlgC, FlgF, FlgG, and FliE, flagellar basal body proteins of Salmonella
    • 10.1016/j.jmb.2004.03.070 15136044
    • Saijo-Hamano Y Uchida N Namba K Oosawa K In vitro characterization of FlgB, FlgC, FlgF, FlgG, and FliE, flagellar basal body proteins of Salmonella. J Mol Biol 2004, 339:423-435. 10.1016/j.jmb.2004.03.070 15136044
    • (2004) J Mol Biol , vol.339 , pp. 423-435
    • Saijo-Hamano, Y.1    Uchida, N.2    Namba, K.3    Oosawa, K.4
  • 34
    • 13444302756 scopus 로고    scopus 로고
    • Pseudomonas aeruginosa Genome Database and PseudoCAP: Facilitating community-based, continually updated, genome annotation
    • Database 540001 15608211
    • Winsor GL Lo R Sui SJ Ung KS Huang S Cheng D Ching WK Hancock RE Brinkman FS Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res 2005, 33(Database):D338-343. 540001 15608211
    • (2005) Nucleic Acids Res , vol.33
    • Winsor, G.L.1    Lo, R.2    Sui, S.J.3    Ung, K.S.4    Huang, S.5    Cheng, D.6    Ching, W.K.7    Hancock, R.E.8    Brinkman, F.S.9
  • 35
    • 46049085923 scopus 로고    scopus 로고
    • Institut Pasteur
    • Institut Pasteur http://genolist.pasteur.fr/SubtiList/
  • 36
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • 403769 14597658 10.1101/gr.1239303
    • Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 403769 14597658 10.1101/gr.1239303
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 37
    • 4444250479 scopus 로고    scopus 로고
    • Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes
    • 519111 15353560 10.1093/nar/gkh815
    • Snel B van Noort V Huynen MA Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucleic Acids Res 2004, 32:4725-4731. 519111 15353560 10.1093/nar/gkh815
    • (2004) Nucleic Acids Res , vol.32 , pp. 4725-4731
    • Snel, B.1    van Noort, V.2    Huynen, M.A.3
  • 38
    • 33747870202 scopus 로고    scopus 로고
    • YOGY: A web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms
    • (Web Server) 1538793 16845020 10.1093/nar/gkl311
    • Penkett CJ Morris JA Wood V Bahler J YOGY: A web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic Acids Res 2006, 34(Web Server):W330-334. 1538793 16845020 10.1093/nar/gkl311
    • (2006) Nucleic Acids Res , vol.34
    • Penkett, C.J.1    Morris, J.A.2    Wood, V.3    Bahler, J.4
  • 39
    • 0034178257 scopus 로고    scopus 로고
    • Homology a personal view on some of the problems
    • 10.1016/S0168-9525(00)02005-9 10782117
    • Fitch WM Homology a personal view on some of the problems. Trends Genet 2000, 16:227-231. 10.1016/S0168-9525(00)02005-9 10782117
    • (2000) Trends Genet , vol.16 , pp. 227-231
    • Fitch, W.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.