메뉴 건너뛰기




Volumn 9, Issue 5, 2008, Pages

Sequence-based prediction of protein-protein interactions by means of codon usage

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CODON USAGE; CONTROLLED STUDY; DNA CONTENT; ESCHERICHIA COLI; NONHUMAN; OPEN READING FRAME; PLASMODIUM FALCIPARUM; PROBABILISTIC INTERACTOME USING CODON USAGE; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; ANIMAL; CODON; EVALUATION; GENETICS; METABOLISM;

EID: 47149115729     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-5-r87     Document Type: Article
Times cited : (67)

References (44)
  • 1
    • 0034660322 scopus 로고    scopus 로고
    • Protein function in the post-genomic era
    • 10.1038/35015694 10866208
    • Eisenberg D Marcotte EM Xenarios I Yeates TO Protein function in the post-genomic era. Nature 2000, 405:823-826 10.1038/35015694 10866208
    • (2000) Nature , vol.405 , pp. 823-826
    • Eisenberg, D.1    Marcotte, E.M.2    Xenarios, I.3    Yeates, T.O.4
  • 2
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • 1847944 17353930 10.1038/msb4100129
    • Sharan R Ulitsky I Shamir R Network-based prediction of protein function. Molecular systems biology 2007, 3:88 1847944 17353930 10.1038/ msb4100129
    • (2007) Molecular Systems Biology , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 4
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • 10427000 10427000 10.1126/science.285.5428.751
    • 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 10427000 10427000 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
  • 7
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein - Protein interactions from primary structure
    • 10.1093/bioinformatics/17.5.455 11331240
    • Bock JR Gough DA Predicting protein - protein interactions from primary structure. Bioinformatics (Oxford, England) 2001, 17:455-460 10.1093/ bioinformatics/17.5.455 11331240
    • (2001) Bioinformatics (Oxford, England) , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 8
    • 33646871614 scopus 로고    scopus 로고
    • An ensemble of K-local hyperplanes for predicting protein-protein interactions
    • 10.1093/bioinformatics/btl055 16481334
    • Nanni L Lumini A An ensemble of K-local hyperplanes for predicting protein-protein interactions. Bioinformatics (Oxford, England) 2006, 22:1207-1210 10.1093/bioinformatics/btl055 16481334
    • (2006) Bioinformatics (Oxford, England) , vol.22 , pp. 1207-1210
    • Nanni, L.1    Lumini, A.2
  • 9
    • 0038476173 scopus 로고    scopus 로고
    • Revisiting the codon adaptation index from a whole-genome perspective: Analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models
    • 153734 12682375 10.1093/nar/gkg306
    • Jansen R Bussemaker HJ Gerstein M Revisiting the codon adaptation index from a whole-genome perspective: Analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic acids research 2003, 31:2242-2251 153734 12682375 10.1093/nar/ gkg306
    • (2003) Nucleic Acids Research , vol.31 , pp. 2242-2251
    • Jansen, R.1    Bussemaker, H.J.2    Gerstein, M.3
  • 10
    • 0037390641 scopus 로고    scopus 로고
    • G+C3 structuring along the genome: A common feature in prokaryotes
    • 10.1093/molbev/msg022
    • Daubin V Perriere G G+C3 structuring along the genome: A common feature in prokaryotes. Molecular biology and evolution 2003, 20:471-483 10.1093/ molbev/msg022
    • (2003) Molecular Biology and Evolution , vol.20 , pp. 471-483
    • Daubin, V.1    Perriere, G.2
  • 11
    • 0038179369 scopus 로고    scopus 로고
    • Selective charging of tRNA isoacceptors explains patterns of codon usage
    • 12805541 12805541 10.1126/science.1083811
    • Elf J Nilsson D Tenson T Ehrenberg M Selective charging of tRNA isoacceptors explains patterns of codon usage. Science. 2003, 300:1718-1722 12805541 12805541 10.1126/science.1083811
    • (2003) Science , vol.300 , pp. 1718-1722
    • Elf, J.1    Nilsson, D.2    Tenson, T.3    Ehrenberg, M.4
  • 12
    • 14644396660 scopus 로고    scopus 로고
    • Selective charging of tRNA isoacceptors induced by amino-acid starvation
    • 1299251 15678157 10.1038/sj.embor.7400341
    • Dittmar KA Sorensen MA Elf J Ehrenberg M Pan T Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO reports 2005, 6:151-157 1299251 15678157 10.1038/sj.embor.7400341
    • (2005) EMBO Reports , vol.6 , pp. 151-157
    • Dittmar, K.A.1    Sorensen, M.A.2    Elf, J.3    Ehrenberg, M.4    Pan, T.5
  • 13
    • 22244447463 scopus 로고    scopus 로고
    • Assessing the limits of genomic data integration for predicting protein networks
    • 1172038 15998909 10.1101/gr.3610305
    • Lu LJ Xia Y Paccanaro A Yu H Gerstein M Assessing the limits of genomic data integration for predicting protein networks. Genome research 2005, 15:945-953 1172038 15998909 10.1101/gr.3610305
    • (2005) Genome Research , vol.15 , pp. 945-953
    • Lu, L.J.1    Xia, Y.2    Paccanaro, A.3    Yu, H.4    Gerstein, M.5
  • 15
    • 14244266085 scopus 로고    scopus 로고
    • Relative predicted protein levels of functionally associated proteins are conserved across organisms
    • 549420 15718304 10.1093/nar/gki261
    • Lithwick G Margalit H Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic acids research 2005, 33:1051-1057 549420 15718304 10.1093/nar/gki261
    • (2005) Nucleic Acids Research , vol.33 , pp. 1051-1057
    • Lithwick, G.1    Margalit, H.2
  • 16
    • 0023650543 scopus 로고
    • The codon Adaptation Index - A measure of directional synonymous codon usage bias, and its potential applications
    • 340524 3547335 10.1093/nar/15.3.1281
    • Sharp PM Li WH The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic acids research 1987, 15:1281-1295 340524 3547335 10.1093/nar/15.3.1281
    • (1987) Nucleic Acids Research , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 17
    • 0033050538 scopus 로고    scopus 로고
    • Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: Compositional constraints and translational selection
    • 10.1007/PL00006531 10368431
    • Musto H Romero H Zavala A Jabbari K Bernardi G Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: Compositional constraints and translational selection. Journal of molecular evolution 1999, 49:27-35 10.1007/PL00006531 10368431
    • (1999) Journal of Molecular Evolution , vol.49 , pp. 27-35
    • Musto, H.1    Romero, H.2    Zavala, A.3    Jabbari, K.4    Bernardi, G.5
  • 18
    • 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, 402:86-90 10.1038/47056 10573422
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 20
    • 0023046874 scopus 로고
    • Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
    • 311530 3526280 10.1093/nar/14.13.5125
    • Sharp PM Tuohy TM Mosurski KR Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic acids research 1986, 14:5125-5143 311530 3526280 10.1093/nar/14.13.5125
    • (1986) Nucleic Acids Research , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.M.2    Mosurski, K.R.3
  • 21
    • 33644784817 scopus 로고    scopus 로고
    • Estimating the "effective number of codons": The Wright way of determining codon homozygosity leads to superior estimates
    • 1456227 16299393 10.1534/genetics.105.049643
    • Fuglsang A Estimating the "effective number of codons": The Wright way of determining codon homozygosity leads to superior estimates. Genetics 2006, 172:1301-1307 1456227 16299393 10.1534/ genetics.105.049643
    • (2006) Genetics Genetics , vol.172 , pp. 1301-1307
    • Fuglsang, A.1
  • 28
    • 33144472700 scopus 로고    scopus 로고
    • Tandem affinity purification revealed the hypusine-dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex
    • 10.1002/jcb.20658 16215987
    • Jao DL Chen KY Tandem affinity purification revealed the hypusine-dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex. Journal of cellular biochemistry 2006, 97:583-598 10.1002/jcb.20658 16215987
    • (2006) Journal of Cellular Biochemistry , vol.97 , pp. 583-598
    • Jao, D.L.1    Chen, K.Y.2
  • 29
    • 0037470057 scopus 로고    scopus 로고
    • Functional interactions between yeast translation eukaryotic elongation factor (eEF) 1A and eEF3
    • 10.1074/jbc.M209224200 12493761
    • Anand M Chakraburtty K Marton MJ Hinnebusch AG Kinzy TG Functional interactions between yeast translation eukaryotic elongation factor (eEF) 1A and eEF3. The Journal of biological chemistry 2003, 278:6985-6991 10.1074/jbc.M209224200 12493761
    • (2003) The Journal of Biological Chemistry , vol.278 , pp. 6985-6991
    • Anand, M.1    Chakraburtty, K.2    Marton, M.J.3    Hinnebusch, A.G.4    Kinzy, T.G.5
  • 30
    • 0026555469 scopus 로고
    • A maturase-encoding group IIA intron of yeast mitochondria self-splices in vitro
    • 312266 1579468 10.1093/nar/20.7.1747
    • Hebbar SK Belcher SM Perlman PS A maturase-encoding group IIA intron of yeast mitochondria self-splices in vitro. Nucleic acids research 1992, 20:1747-1754 312266 1579468 10.1093/nar/20.7.1747
    • (1992) Nucleic Acids Research , vol.20 , pp. 1747-1754
    • Hebbar, S.K.1    Belcher, S.M.2    Perlman, P.S.3
  • 31
    • 0346123001 scopus 로고    scopus 로고
    • Two for the price of one: A bifunctional intron-encoded DNA endonuclease-RNA maturase
    • 10.1101/gad.1162503 14665667
    • Belfort M Two for the price of one: A bifunctional intron-encoded DNA endonuclease-RNA maturase. Genes & development 2003, 17:2860-2863 10.1101/gad.1162503 14665667
    • (2003) Genes & Development , vol.17 , pp. 2860-2863
    • Belfort, M.1
  • 33
    • 34547102278 scopus 로고    scopus 로고
    • Human RNase P: A tRNA-processing enzyme and transcription factor
    • 1920233 17483522 10.1093/nar/gkm071
    • Jarrous N Reiner R Human RNase P: A tRNA-processing enzyme and transcription factor. Nucleic acids research 2007, 35:3519-3524 1920233 17483522 10.1093/nar/gkm071
    • (2007) Nucleic Acids Research , vol.35 , pp. 3519-3524
    • Jarrous, N.1    Reiner, R.2
  • 34
    • 33745123379 scopus 로고    scopus 로고
    • A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription
    • 1482482 16778078 10.1101/gad.386706
    • Reiner R Ben-Asouli Y Krilovetzky I Jarrous N A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription. Genes & development 2006, 20:1621-1635 1482482 16778078 10.1101/gad.386706
    • (2006) Genes & Development , vol.20 , pp. 1621-1635
    • Reiner, R.1    Ben-Asouli, Y.2    Krilovetzky, I.3    Jarrous, N.4
  • 35
    • 0033869355 scopus 로고    scopus 로고
    • Nonrandom spatial distribution of synonymous substitutions in the GP63 gene from Leishmania
    • 1461213 10924466
    • Alvarez-Valin F Tort JF Bernardi G Nonrandom spatial distribution of synonymous substitutions in the GP63 gene from Leishmania. Genetics 2000, 155:1683-1692 1461213 10924466
    • (2000) Genetics , vol.155 , pp. 1683-1692
    • Alvarez-Valin, F.1    Tort, J.F.2    Bernardi, G.3
  • 36
    • 47149099325 scopus 로고    scopus 로고
    • ftp://genome-ftp.stanford.edu/pub/yeast/sequence/genomic_sequence/ orf_dna/orf_coding_all.fasta.gz
    • Saccharomyces cerevisiae coding sequences ftp://genome-ftp.stanford.edu/ pub/yeast/sequence/genomic_sequence/orf_dna/orf_coding_all.fasta.gz
    • Saccharomyces Cerevisiae Coding Sequences
  • 38
    • 47149089617 scopus 로고    scopus 로고
    • Plasmodium falciparum coding sequences http://www.plasmodb.org/common/ downloads/release-5.4/Pfalciparum/ PfalciparumAnnotatedCDS_plasmoDB-5.4.fasta
    • Plasmodium Falciparum Coding Sequences
  • 39
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 10.1038/nature01644 12748633
    • Kellis M Patterson N Endrizzi M Birren B Lander ES Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254 10.1038/nature01644 12748633
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 40
    • 0035999672 scopus 로고    scopus 로고
    • Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts
    • 10.1093/bioinformatics/18.4.585 12016056
    • Greenbaum D Jansen R Gerstein M Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics (Oxford, England) 2002, 18:585-596 10.1093/bioinformatics/ 18.4.585 12016056
    • (2002) Bioinformatics (Oxford, England) , vol.18 , pp. 585-596
    • Greenbaum, D.1    Jansen, R.2    Gerstein, M.3
  • 43
    • 33645510456 scopus 로고    scopus 로고
    • Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale
    • 1457034 16520460 10.1101/gr.4573206
    • Date SV Stoeckert CJ Jr Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. Genome research 2006, 16:542-549 1457034 16520460 10.1101/gr.4573206
    • (2006) Genome Research , vol.16 , pp. 542-549
    • Date, S.V.1    Stoeckert Jr., C.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.