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Volumn 3, Issue 11, 2002, Pages

The society of genes: networks of functional links between genes from comparative genomics

Author keywords

Additional Data File; Cluster Coefficient; Functional Link; Phylogenetic Profile; Random Network

Indexed keywords

ARTICLE; CHROMOSOME; COMPARATIVE GENOMICS; CONTROLLED STUDY; FEMALE; GENE; GENOME SIZE; HUMAN; MICROBIAL GENOME; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; CHROMOSOME MAP; COMPARATIVE STUDY; GENETICS; GENOMICS; METHODOLOGY; MULTIGENE FAMILY; PHYLOGENY; PHYSIOLOGY; SYNTENY;

EID: 0037174738     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2002-3-11-research0064     Document Type: Article
Times cited : (46)

References (42)
  • 2
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • PID: 9623998, COI: 1:CAS:528:DyaK1cXjs1Khsrk%3D
    • Watts DJ, Strogatz SH: Collective dynamics of 'small-world' networks. Nature. 1998, 393: 440-442. 10.1038/30918. DOI: 10.1038/30918
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 3
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • PID: 10521342
    • Barabasi AL, Albert R: Emergence of scaling in random networks. Science. 1999, 286: 509-512. 10.1126/science.286.5439.509. DOI: 10.1126/science.286.5439.509
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 5
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • PID: 11283351, COI: 1:CAS:528:DC%2BD3MXjtVagtLc%3D
    • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA. 2001, 98: 4569-4574. 10.1073/pnas.061034498. DOI: 10.1073/pnas.061034498
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5    Sakaki, Y.6
  • 6
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • PID: 11805826, COI: 1:CAS:528:DC%2BD38XmsVCgtw%3D%3D
    • Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, et al: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002, 415: 141-147. 10.1038/415141a. DOI: 10.1038/415141a
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5    Bauer, A.6    Schultz, J.7    Rick, J.M.8    Michon, A.M.9    Cruciat, C.M.10
  • 7
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiaeby mass spectrometry
    • PID: 11805837, COI: 1:CAS:528:DC%2BD38Xms1SnsA%3D%3D
    • Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, et al: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002, 415: 180-183. 10.1038/415180a. DOI: 10.1038/415180a
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.D.4    Moore, L.5    Adams, S.L.6    Millar, A.7    Taylor, P.8    Bennett, K.9    Boutilier, K.10
  • 8
    • 0034084865 scopus 로고    scopus 로고
    • Who's your neighbor? New computational approaches for functional genomics
    • PID: 10835597, COI: 1:CAS:528:DC%2BD3cXkt12gtr8%3D
    • Galperin MY, Koonin EV: Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol. 2000, 18: 609-613. 10.1038/76443. DOI: 10.1038/76443
    • (2000) Nat Biotechnol , vol.18 , pp. 609-613
    • Galperin, M.Y.1    Koonin, E.V.2
  • 9
    • 0034072743 scopus 로고    scopus 로고
    • Exploitation of gene context
    • PID: 10851194, COI: 1:CAS:528:DC%2BD3cXktlyksLY%3D
    • Huynen M, Snel B, Lathe W, Bork P: Exploitation of gene context. Curr Opin Struct Biol. 2000, 10: 366-370. 10.1016/S0959-440X(00)00098-1. DOI: 10.1016/S0959-440X(00)00098-1
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 366-370
    • Huynen, M.1    Snel, B.2    Lathe, W.3    Bork, P.4
  • 10
    • 0034660322 scopus 로고    scopus 로고
    • Protein function in the post-genomic era
    • PID: 10866208, COI: 1:CAS:528:DC%2BD3cXksVyksLw%3D
    • Eisenberg D, Marcotte EM, Xenarios I, Yeates TO: Protein function in the post-genomic era. Nature. 2000, 405: 823-836. 10.1038/35015694. DOI: 10.1038/35015694
    • (2000) Nature , vol.405 , pp. 823-836
    • Eisenberg, D.1    Marcotte, E.M.2    Xenarios, I.3    Yeates, T.O.4
  • 11
    • 0034027595 scopus 로고    scopus 로고
    • Computational genetics: finding protein function by nonhomology methods
    • PID: 10851184, COI: 1:CAS:528:DC%2BD3cXktlyksLk%3D
    • Marcotte EM: Computational genetics: finding protein function by nonhomology methods. Curr Opin Struct Biol. 2000, 10: 359-365. 10.1016/S0959-440X(00)00097-X. DOI: 10.1016/S0959-440X(00)00097-X
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 359-365
    • Marcotte, E.M.1
  • 12
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • PID: 9381173, COI: 1:CAS:528:DyaK2sXmvVOrsL0%3D
    • Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science. 1997, 278: 631-637. 10.1126/science.278.5338.631. DOI: 10.1126/science.278.5338.631
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 13
    • 0031610846 scopus 로고    scopus 로고
    • Constructing multigenome views of whole microbial genomes
    • PID: 9775388, COI: 1:CAS:528:DyaK1cXmt1OisL4%3D
    • Gaasterland T, Ragan MA: Constructing multigenome views of whole microbial genomes. Microb Comp Genomics. 1998, 3: 177-192. DOI: 10.1089/omi.1.1998.3.177
    • (1998) Microb Comp Genomics , vol.3 , pp. 177-192
    • Gaasterland, T.1    Ragan, M.A.2
  • 14
    • 0033551248 scopus 로고    scopus 로고
    • Assigning protein functions by comparative genome analysis: protein phylogenetic profiles
    • PID: 10200254, COI: 1:CAS:528:DyaK1MXjs1ymurs%3D
    • 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. 10.1073/pnas.96.8.4285. DOI: 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
  • 15
    • 0030809629 scopus 로고    scopus 로고
    • Selfish operons and speciation by gene transfer
    • PID: 9294891, COI: 1:STN:280:DyaK2svktVKksQ%3D%3D
    • Lawrence JG: Selfish operons and speciation by gene transfer. Trends Microbiol. 1997, 5: 355-359. 10.1016/S0966-842X(97)01110-4. DOI: 10.1016/S0966-842X(97)01110-4
    • (1997) Trends Microbiol , vol.5 , pp. 355-359
    • Lawrence, J.G.1
  • 16
    • 0033055062 scopus 로고    scopus 로고
    • The use of gene clusters to infer functional coupling
    • PID: 10077608, COI: 1:CAS:528:DyaK1MXhvFyks7s%3D
    • Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N: The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA. 1999, 96: 2896-2901. 10.1073/pnas.96.6.2896. DOI: 10.1073/pnas.96.6.2896
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 2896-2901
    • Overbeek, R.1    Fonstein, M.2    D'Souza, M.3    Pusch, G.D.4    Maltsev, N.5
  • 17
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: a fingerprint of proteins that physically interact
    • PID: 9787636, COI: 1:CAS:528:DyaK1cXmsVWmtrw%3D
    • Dandekar T, Snel B, Huynen M, Bork P: Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 1998, 23: 324-328. 10.1016/S0968-0004(98)01274-2. DOI: 10.1016/S0968-0004(98)01274-2
    • (1998) Trends Biochem Sci , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 18
    • 0034668036 scopus 로고    scopus 로고
    • Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping
    • PID: 11024184, COI: 1:CAS:528:DC%2BD3cXns1akt7Y%3D
    • Fujibuchi W, Ogata H, Matsuda H, Kanehisa M: Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. Nucleic Acids Res. 2000, 28: 4029-4036. 10.1093/nar/28.20.4029. DOI: 10.1093/nar/28.20.4029
    • (2000) Nucleic Acids Res , vol.28 , pp. 4029-4036
    • Fujibuchi, W.1    Ogata, H.2    Matsuda, H.3    Kanehisa, M.4
  • 19
    • 0036533931 scopus 로고    scopus 로고
    • Identifying functional links between genes using conserved chromosomal proximity
    • PID: 11932011, COI: 1:CAS:528:DC%2BD38XisV2htLs%3D
    • Yanai I, Mellor JC, DeLisi C: Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 2002, 18: 176-179. 10.1016/S0168-9525(01)02621-X. DOI: 10.1016/S0168-9525(01)02621-X
    • (2002) Trends Genet , vol.18 , pp. 176-179
    • Yanai, I.1    Mellor, J.C.2    DeLisi, C.3
  • 20
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • PID: 10427000, COI: 1:CAS:528:DyaK1MXltVehtbg%3D
    • 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. DOI: 10.1126/science.285.5428.751
    • (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
  • 21
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • PID: 10573422, COI: 1:CAS:528:DyaK1MXntlCms7s%3D
    • Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA: Protein interaction maps for complete genomes based on gene fusion events. Nature. 1999, 402: 86-90. DOI: 10.1038/47056
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 22
    • 0034940467 scopus 로고    scopus 로고
    • Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes
    • PID: 11438739, COI: 1:CAS:528:DC%2BD3MXlt1KntLw%3D
    • Yanai I, Derti A, DeLisi C: Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc Natl Acad Sci USA. 2001, 98: 7940-7945. 10.1073/pnas.141236298. DOI: 10.1073/pnas.141236298
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 7940-7945
    • Yanai, I.1    Derti, A.2    DeLisi, C.3
  • 23
    • 0035753236 scopus 로고    scopus 로고
    • Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions
    • Enright AJ, Ouzounis CA: Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol. 2001, 2: 1-0034. 10.1186/gb-2001-2-9-research0034. DOI: 10.1186/gb-2001-2-9-research0034
    • (2001) Genome Biol , vol.2 , pp. 1-0034
    • Enright, A.J.1    Ouzounis, C.A.2
  • 24
    • 0036081482 scopus 로고    scopus 로고
    • Predictome: a database of putative functional links between proteins
    • PID: 11752322, COI: 1:CAS:528:DC%2BD38Xht12rs7w%3D
    • 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. 10.1093/nar/30.1.306. DOI: 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
  • 25
    • 0034887573 scopus 로고    scopus 로고
    • Scale-free behavior in protein domain networks
    • PID: 11504849, COI: 1:CAS:528:DC%2BD3MXmt12iu7g%3D
    • Wuchty S: Scale-free behavior in protein domain networks. Mol Biol Evol. 2001, 18: 1694-1702. DOI: 10.1093/oxfordjournals.molbev.a003957
    • (2001) Mol Biol Evol , vol.18 , pp. 1694-1702
    • Wuchty, S.1
  • 26
    • 0035816218 scopus 로고    scopus 로고
    • Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    • PID: 11428892, COI: 1:CAS:528:DC%2BD3MXks1OrsLc%3D
    • Apic G, Gough J, Teichmann SA: Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. 2001, 310: 311-325. 10.1006/jmbi.2001.4776. DOI: 10.1006/jmbi.2001.4776
    • (2001) J Mol Biol , vol.310 , pp. 311-325
    • Apic, G.1    Gough, J.2    Teichmann, S.A.3
  • 27
    • 0035232163 scopus 로고    scopus 로고
    • An insight into domain combinations
    • PID: 11472996
    • Apic G, Gough J, Teichmann SA: An insight into domain combinations. Bioinformatics. 2001, 17: S83-S89. 10.1093/bioinformatics/17.1.83. DOI: 10.1093/bioinformatics/17.suppl_1.S83
    • (2001) Bioinformatics , vol.17 , pp. S83-S89
    • Apic, G.1    Gough, J.2    Teichmann, S.A.3
  • 28
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: quantitative evaluation and qualitative inferences
    • PID: 10958638, COI: 1:CAS:528:DC%2BD3cXmtFels7w%3D
    • Huynen M, Snel B, Lathe W, Bork P: Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 2000, 10: 1204-1210. 10.1101/gr.10.8.1204. DOI: 10.1101/gr.10.8.1204
    • (2000) Genome Res , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe, W.3    Bork, P.4
  • 29
    • 0033523854 scopus 로고    scopus 로고
    • A combined algorithm for genome-wide prediction of protein function
    • PID: 10573421, COI: 1:CAS:528:DyaK1MXntlCms78%3D
    • Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D: A combined algorithm for genome-wide prediction of protein function. Nature. 1999, 402: 83-86. 10.1038/47048. DOI: 10.1038/47048
    • (1999) Nature , vol.402 , pp. 83-86
    • Marcotte, E.M.1    Pellegrini, M.2    Thompson, M.J.3    Yeates, T.O.4    Eisenberg, D.5
  • 30
    • 0037197886 scopus 로고    scopus 로고
    • The identification of functional modules from the genomic association of genes
    • PID: 11983890, COI: 1:CAS:528:DC%2BD38XjslWgtLY%3D
    • Snel B, Bork P, Huynen MA: The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA. 2002, 99: 5890-5895. 10.1073/pnas.092632599. DOI: 10.1073/pnas.092632599
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5890-5895
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 31
    • 0034633749 scopus 로고    scopus 로고
    • Classes of small-world networks
    • PID: 11005838, COI: 1:CAS:528:DC%2BD3cXnsF2rt7g%3D
    • Amaral LA, Scala A, Barthelemy M, Stanley HE: Classes of small-world networks. Proc Natl Acad Sci USA. 2000, 97: 11149-11152. 10.1073/pnas.200327197. DOI: 10.1073/pnas.200327197
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 11149-11152
    • Amaral, L.A.1    Scala, A.2    Barthelemy, M.3    Stanley, H.E.4
  • 33
    • 0035836771 scopus 로고    scopus 로고
    • Networking proteins in yeast
    • PID: 11296274, COI: 1:CAS:528:DC%2BD3MXjtVags7o%3D
    • Hazbun TR, Fields S: Networking proteins in yeast. Proc Natl Acad Sci USA. 2001, 98: 4277-42778. 10.1073/pnas.091096398. DOI: 10.1073/pnas.091096398
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4277-42778
    • Hazbun, T.R.1    Fields, S.2
  • 34
    • 0035279936 scopus 로고    scopus 로고
    • Towards an understanding of complex protein networks
    • PID: 11306254, COI: 1:CAS:528:DC%2BD3MXisVGrsLo%3D
    • Tucker CL, Gera JF, Uetz P: Towards an understanding of complex protein networks. Trends Cell Biol. 2001, 11: 102-106. 10.1016/S0962-8924(00)01902-4. DOI: 10.1016/S0962-8924(00)01902-4
    • (2001) Trends Cell Biol , vol.11 , pp. 102-106
    • Tucker, C.L.1    Gera, J.F.2    Uetz, P.3
  • 35
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • PID: 12000970, COI: 1:CAS:528:DC%2BD38XktVSrt7o%3D
    • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002, 417: 399-403. 10.1038/nature750. DOI: 10.1038/nature750
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 36
    • 85182641818 scopus 로고    scopus 로고
    • Predictome. [http://predictome.bu.edu]
    • Predictome
  • 38
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • PID: 9254694, COI: 1:CAS:528:DyaK2sXlvFyhu7w%3D
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389. DOI: 10.1093/nar/25.17.3389
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 39
    • 0031829372 scopus 로고    scopus 로고
    • Removing near-neighbour redundancy from large protein sequence collections
    • PID: 9682055, COI: 1:CAS:528:DyaK1cXlsFKru74%3D
    • Holm L, Sander C: Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics. 1998, 14: 423-429. 10.1093/bioinformatics/14.5.423. DOI: 10.1093/bioinformatics/14.5.423
    • (1998) Bioinformatics , vol.14 , pp. 423-429
    • Holm, L.1    Sander, C.2
  • 40
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • PID: 10592173, COI: 1:CAS:528:DC%2BD3cXhvVGqu74%3D
    • Kanehisa M, Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093/nar/28.1.27. DOI: 10.1093/nar/28.1.27
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2


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