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Volumn 2, Issue , 2008, Pages

The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; HOMO SAPIENS; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; SACCHAROMYCES CEREVISIAE;

EID: 53149088565     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-80     Document Type: Article
Times cited : (64)

References (56)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • 10.1038/nrg1272 14735121
    • Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization Nat Rev Genet 2004, 5(2):101-113 10.1038/nrg1272 14735121
    • (2004) Nat Rev Genet , vol.5 , Issue.2 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 2
    • 27944493925 scopus 로고    scopus 로고
    • Scale-free networks in cell biology
    • 10.1242/jcs.02714 16254242
    • Albert R Scale-free networks in cell biology J Cell Sci 2005, 118(Pt 21):4947-4957 10.1242/jcs.02714 16254242
    • (2005) J Cell Sci , vol.118 , Issue.PART 21 , pp. 4947-4957
    • Albert, R.1
  • 4
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • 31875 11283351 10.1073/pnas.061034498
    • 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(8):4569-4574 31875 11283351 10.1073/pnas.061034498
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.8 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5    Sakaki, Y.6
  • 15
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • 10.1038/35019019 10935628
    • Albert R Jeong H Barabasi AL Error and attack tolerance of complex networks Nature 2000, 406(6794):378-382 10.1038/35019019 10935628
    • (2000) Nature , vol.406 , Issue.6794 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.L.3
  • 16
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • 10.1038/35075138 11333967
    • Jeong H Mason SP Barabasi AL Oltvai ZN Lethality and centrality in protein networks Nature 2001, 411(6833):41-42 10.1038/35075138 11333967
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 17
    • 33745712594 scopus 로고    scopus 로고
    • Why do hubs tend to be essential in protein networks?
    • 1473040 16751849 10.1371/journal.pgen.0020088
    • He X Zhang J Why do hubs tend to be essential in protein networks? PLoS Genet 2006, 2(6):e88 1473040 16751849 10.1371/journal.pgen.0020088
    • (2006) PLoS Genet , vol.2 , Issue.6
    • He, X.1    Zhang, J.2
  • 18
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • 10.1016/S0968-0004(98)01274-2 9787636
    • Dandekar T Snel B Huynen M Bork P Conservation of gene order: A fingerprint of proteins that physically interact Trends Biochem Sci 1998, 23(9):324-328 10.1016/S0968-0004(98)01274-2 9787636
    • (1998) Trends Biochem Sci , vol.23 , Issue.9 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 19
    • 0033055062 scopus 로고    scopus 로고
    • The use of gene clusters to infer functional coupling
    • 15866 10077608 10.1073/pnas.96.6.2896
    • 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(6):2896-2901 15866 10077608 10.1073/pnas.96.6.2896
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.6 , pp. 2896-2901
    • Overbeek, R.1    Fonstein, M.2    D'Souza, M.3    Pusch, G.D.4    Maltsev, N.5
  • 20
    • 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(5428):751-753 10.1126/science.285.5428.751 10427000
    • (1999) Science , vol.285 , Issue.5428 , 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
    • 10.1038/47056 10573422
    • Enright AJ Iliopoulos I Kyrpides NC Ouzounis CA Protein interaction maps for complete genomes based on gene fusion events Nature 1999, 402(6757):86-90 10.1038/47056 10573422
    • (1999) Nature , vol.402 , Issue.6757 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 22
    • 0035733690 scopus 로고    scopus 로고
    • Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
    • 10.1038/ng776 11694880
    • Ge H Liu Z Church GM Vidal M Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae Nat Genet 2001, 29(4):482-486 10.1038/ng776 11694880
    • (2001) Nat Genet , vol.29 , Issue.4 , pp. 482-486
    • Ge, H.1    Liu, Z.2    Church, G.M.3    Vidal, M.4
  • 23
    • 0035445792 scopus 로고    scopus 로고
    • A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae
    • 55876 11522820 10.1093/nar/29.17.3513
    • Grigoriev A A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae Nucleic Acids Res 2001, 29(17):3513-3519 55876 11522820 10.1093/nar/29.17.3513
    • (2001) Nucleic Acids Res , vol.29 , Issue.17 , pp. 3513-3519
    • Grigoriev, A.1
  • 24
    • 0036141992 scopus 로고    scopus 로고
    • Relating whole-genome expression data with protein-protein interactions
    • 155252 11779829 10.1101/gr.205602
    • Jansen R Greenbaum D Gerstein M Relating whole-genome expression data with protein-protein interactions Genome Res 2002, 12(1):37-46 155252 11779829 10.1101/gr.205602
    • (2002) Genome Res , vol.12 , Issue.1 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 25
    • 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(8):4285-4288 16324 10200254 10.1073/pnas.96.8.4285
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.8 , pp. 4285-4288
    • Pellegrini, M.1    Marcotte, E.M.2    Thompson, M.J.3    Eisenberg, D.4    Yeates, T.O.5
  • 26
    • 0035211290 scopus 로고    scopus 로고
    • 311221 11731503 10.1101/gr.205301
    • Matthews LR Vaglio P Reboul J Ge H Davis BP Garrels J Vincent S Vidal M Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs" Genome Res 2001, 11(12):2120-2126 311221 11731503 10.1101/gr.205301
    • (2001) Genome Res , vol.11 , Issue.12 , pp. 2120-2126
    • Matthews, L.R.1    Vaglio, P.2    Reboul, J.3    Ge, H.4    Davis, B.P.5    Garrels, J.6    Vincent, S.7    Vidal, M.8
  • 27
    • 0036360139 scopus 로고    scopus 로고
    • Towards the prediction of complete protein - Protein interaction networks
    • 11928495
    • Gomez SM Rzhetsky A Towards the prediction of complete protein - protein interaction networks Pac Symp Biocomput 2002, 413-424 11928495
    • (2002) Pac Symp Biocomput , pp. 413-424
    • Gomez, S.M.1    Rzhetsky, A.2
  • 28
    • 0038620469 scopus 로고    scopus 로고
    • Integrative approach for computationally inferring protein domain interactions
    • 10.1093/bioinformatics/btg118 12761053
    • Ng SK Zhang Z Tan SH Integrative approach for computationally inferring protein domain interactions Bioinformatics 2003, 19(8):923-929 10.1093/ bioinformatics/btg118 12761053
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 923-929
    • Ng, S.K.1    Zhang, Z.2    Tan, S.H.3
  • 29
    • 3242701661 scopus 로고    scopus 로고
    • Computational prediction of protein-protein interactions
    • 15064475
    • Obenauer JC Yaffe MB Computational prediction of protein-protein interactions Methods Mol Biol 2004, 261:445-468 15064475
    • (2004) Methods Mol Biol , vol.261 , pp. 445-468
    • Obenauer, J.C.1    Yaffe, M.B.2
  • 30
    • 12144276041 scopus 로고    scopus 로고
    • Predicting protein-peptide interactions via a network-based motif sampler
    • 10.1093/bioinformatics/bth922 15262809
    • Reiss DJ Schwikowski B Predicting protein-peptide interactions via a network-based motif sampler Bioinformatics 2004, (20 Suppl 1):I274-282 10.1093/bioinformatics/bth922 15262809
    • (2004) Bioinformatics , vol.20 , Issue.20 SUPPL. 1
    • Reiss, D.J.1    Schwikowski, B.2
  • 31
    • 0037110589 scopus 로고    scopus 로고
    • MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
    • 10.1002/prot.10222 12360525
    • Lu L Lu H Skolnick J MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading Proteins 2002, 49(3):350-364 10.1002/prot.10222 12360525
    • (2002) Proteins , vol.49 , Issue.3 , pp. 350-364
    • Lu, L.1    Lu, H.2    Skolnick, J.3
  • 32
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • 122873 11972061 10.1073/pnas.092147999
    • Aloy P Russell RB Interrogating protein interaction networks through structural biology Proc Natl Acad Sci USA 2002, 99(9):5896-5901 122873 11972061 10.1073/pnas.092147999
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.9 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 33
    • 1842559914 scopus 로고    scopus 로고
    • Extracting human protein interactions from MEDLINE using a full-sentence parser
    • 10.1093/bioinformatics/btg452 15033866
    • Daraselia N Yuryev A Egorov S Novichkova S Nikitin A Mazo I Extracting human protein interactions from MEDLINE using a full-sentence parser Bioinformatics 2004, 20(5):604-611 10.1093/bioinformatics/btg452 15033866
    • (2004) Bioinformatics , vol.20 , Issue.5 , pp. 604-611
    • Daraselia, N.1    Yuryev, A.2    Egorov, S.3    Novichkova, S.4    Nikitin, A.5    Mazo, I.6
  • 34
    • 27744543196 scopus 로고    scopus 로고
    • Text mining for metabolic pathways, signaling cascades, and protein networks
    • 10.1126/stke.2832005pe21 15886388
    • Hoffmann R Krallinger M Andres E Tamames J Blaschke C Valencia A Text mining for metabolic pathways, signaling cascades, and protein networks Sci STKE 2005, 2005(283):pE21 10.1126/stke.2832005pe21 15886388
    • (2005) Sci STKE , vol.2005 , Issue.283
    • Hoffmann, R.1    Krallinger, M.2    Andres, E.3    Tamames, J.4    Blaschke, C.5    Valencia, A.6
  • 35
    • 33646018046 scopus 로고    scopus 로고
    • Evaluation of different biological data and computational classification methods for use in protein interaction prediction
    • 10.1002/prot.20865 164503630
    • Qi Y Bar-Joseph Z Klein-Seetharaman J Evaluation of different biological data and computational classification methods for use in protein interaction prediction Proteins 2006, 63(3):490-500 10.1002/prot.20865 164503630
    • (2006) Proteins , vol.63 , Issue.3 , pp. 490-500
    • Qi, Y.1    Bar-Joseph, Z.2    Klein-Seetharaman, J.3
  • 38
    • 45549107329 scopus 로고    scopus 로고
    • Use and misuse of the gene ontology annotations
    • 10.1038/nrg2363 18475267
    • Rhee SY Wood V Dolinski K Draghici S Use and misuse of the gene ontology annotations Nat Rev Genet 2008, 9(7):509-515 10.1038/nrg2363 18475267
    • (2008) Nat Rev Genet , vol.9 , Issue.7 , pp. 509-515
    • Rhee, S.Y.1    Wood, V.2    Dolinski, K.3    Draghici, S.4
  • 42
    • 53149132566 scopus 로고    scopus 로고
    • Go Slim http://www.geneontology.org/GO.slims.shtml
    • Go Slim
  • 43
    • 53149126288 scopus 로고    scopus 로고
    • map2slim
    • map2slim http://search.cpan.org/~cmungall/go-perl/scripts/map2slim
  • 46
    • 53149092245 scopus 로고    scopus 로고
    • STATISTICA http://www.statsoft.com/
    • STATISTICA
  • 49
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • 35 Database 1716718 17130148 10.1093/nar/gkl842
    • Pruitt KD Tatusova T Maglott DR NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res 2007, 35 Database D61-65 1716718 17130148 10.1093/nar/gkl842
    • (2007) Nucleic Acids Res
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 50
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • 10.1006/jmbi.2000.5197 11743721
    • Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001, 314(5):1041-1052 10.1006/jmbi.2000.5197 11743721
    • (2001) J Mol Biol , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 52
    • 53149122232 scopus 로고    scopus 로고
    • HMMER http://hmmer.janelia.org/
    • HMMER
  • 53
    • 0037250151 scopus 로고    scopus 로고
    • InterDom: A database of putative interacting protein domains for validating predicted protein interactions and complexes
    • 165526 12519994 10.1093/nar/gkg079
    • Ng SK Zhang Z Tan SH Lin K InterDom: A database of putative interacting protein domains for validating predicted protein interactions and complexes Nucleic Acids Res 2003, 31(1):251-254 165526 12519994 10.1093/ nar/gkg079
    • (2003) Nucleic Acids Res , vol.31 , Issue.1 , pp. 251-254
    • Ng, S.K.1    Zhang, Z.2    Tan, S.H.3    Lin, K.4
  • 54
    • 13844264506 scopus 로고    scopus 로고
    • iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    • 10.1093/bioinformatics/bti011 15353450
    • Finn RD Marshall M Bateman A iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions Bioinformatics 2005, 21(3):410-412 10.1093/bioinformatics/bti011 15353450
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 410-412
    • Finn, R.D.1    Marshall, M.2    Bateman, A.3
  • 55
    • 0029838985 scopus 로고    scopus 로고
    • Modeling prevention strategies for gonorrhea and Chlamydia using stochastic network simulations
    • 8686700
    • Kretzschmar M van Duynhoven YT Severijnen AJ Modeling prevention strategies for gonorrhea and Chlamydia using stochastic network simulations Am J Epidemiol 1996, 144(3):306-317 8686700
    • (1996) Am J Epidemiol , vol.144 , Issue.3 , pp. 306-317
    • Kretzschmar, M.1    van Duynhoven, Y.T.2    Severijnen, A.J.3
  • 56
    • 0034252172 scopus 로고    scopus 로고
    • Ring vaccination
    • 10.1007/s002850070003 11039695
    • Muller J Schonfisch B Kirkilionis M Ring vaccination J Math Biol 2000, 41(2):143-171 10.1007/s002850070003 11039695
    • (2000) J Math Biol , vol.41 , Issue.2 , pp. 143-171
    • Muller, J.1    Schonfisch, B.2    Kirkilionis, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.