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Volumn 111, Issue 30, 2014, Pages

Proteome-wide remodeling of protein location and function by stress

Author keywords

Bioinformatics; DTT and MMS; Dynamic function prediction; Protein translocation; Systems biology

Indexed keywords

CCR4 ASSOCIATED FACTOR 120; DICARBOXYLIC AMINO ACID PERMEASE 5; DNA; DNA DIRECTED RNA POLYMERASE; IME2 DEPENDENT SIGNALING 2 PROTEIN; INOSITOL REQUIRING 2 PROTEIN; LOW TEMPERATURE ESSENTIAL 1 PROTEIN; NECESSARY FOR NUCLEAR FUNCTION 2 PROTEIN; PERMEASE; PROTEIN; PROTEOME; RNA POLYMERASE I SUBUNIT A43; SUPPRESSOR OF LETHALITY OF KEX2 GAS1 DOUBLE NULL MUTANT 6 PROTEIN; TWENTY S RRNA ACCUMULATION 1 PROTEIN; UNCLASSIFIED DRUG;

EID: 84905014024     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1318881111     Document Type: Article
Times cited : (12)

References (47)
  • 1
    • 84863012289 scopus 로고    scopus 로고
    • PKCe promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria
    • Lau E, et al. (2012) PKCe promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell 148(3):543-555.
    • (2012) Cell , vol.148 , Issue.3 , pp. 543-555
    • Lau, E.1
  • 2
    • 0142184341 scopus 로고    scopus 로고
    • Global analysis of protein localization in budding yeast
    • Huh WK, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-691.
    • (2003) Nature , vol.425 , Issue.6959 , pp. 686-691
    • Huh, W.K.1
  • 6
    • 34547560275 scopus 로고    scopus 로고
    • WoLF PSORT: Protein localization predictor
    • Horton P, et al. (2007) WoLF PSORT: Protein localization predictor. Nucleic Acids Res 35(Web Server Issue):W585-W587.
    • (2007) Nucleic Acids Res , vol.35 , Issue.WEB SERVER ISSUE
    • Horton, P.1
  • 7
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski B, Uetz P, Fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18(12):1257-1261.
    • (2000) Nat Biotechnol , vol.18 , Issue.12 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 8
    • 6344283102 scopus 로고    scopus 로고
    • Predicting subcellular localization via protein motif co-occurrence
    • DOI 10.1101/gr.2650004
    • Scott MS, Thomas DY, Hallett MT (2004) Predicting subcellular localization via protein motif co-occurrence. Genome Res 14(10A):1957-1966. (Pubitemid 39386510)
    • (2004) Genome Research , vol.14 , Issue.10 A , pp. 1957-1966
    • Scott, M.S.1    Thomas, D.Y.2    Hallett, M.T.3
  • 9
    • 33750245540 scopus 로고    scopus 로고
    • PLPD: Reliable protein localization prediction from imbalanced and overlapped datasets
    • DOI 10.1093/nar/gkl638
    • Lee K, Kim DW, Na D, Lee KH, Lee D (2006) PLPD: Reliable protein localization prediction from imbalanced and overlapped datasets. Nucleic Acids Res 34(17):4655-4666. (Pubitemid 44607802)
    • (2006) Nucleic Acids Research , vol.34 , Issue.17 , pp. 4655-4666
    • Lee, K.1    Kim, D.-W.2    Na, D.3    Lee, K.H.4    Lee, D.5
  • 11
    • 20444450051 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structural data
    • DOI 10.1016/j.sbi.2005.04.003, PII S0959440X05000825
    • Watson JD, Laskowski RA, Thornton JM (2005) Predicting protein function from sequence and structural data. Curr Opin Struct Biol 15(3):275-284. (Pubitemid 40826446)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 SPEC. ISS. , pp. 275-284
    • Watson, J.D.1    Laskowski, R.A.2    Thornton, J.M.3
  • 12
    • 48249113702 scopus 로고    scopus 로고
    • Predicting protein function from domain content
    • Forslund K, Sonnhammer EL (2008) Predicting protein function from domain content. Bioinformatics 24(15):1681-1687.
    • (2008) Bioinformatics , vol.24 , Issue.15 , pp. 1681-1687
    • Forslund, K.1    Sonnhammer, E.L.2
  • 13
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • DOI 10.1038/nrm2281, PII NRM2281
    • Lee D, Redfern O, Orengo C (2007) Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 8(12):995-1005. (Pubitemid 350174637)
    • (2007) Nature Reviews Molecular Cell Biology , vol.8 , Issue.12 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 14
    • 16244383493 scopus 로고    scopus 로고
    • Predicting enzyme function from protein sequence
    • DOI 10.1016/j.cbpa.2005.02.003, Bioorganic Chemistry / Biocatalysis and Biotransformation
    • Minshull J, Ness JE, Gustafsson C, Govindarajan S (2005) Predicting enzyme function from protein sequence. Curr Opin Chem Biol 9(2):202-209. (Pubitemid 40462491)
    • (2005) Current Opinion in Chemical Biology , vol.9 , Issue.2 , pp. 202-209
    • Minshull, J.1    Ness, J.E.2    Gustafsson, C.3    Govindarajan, S.4
  • 16
    • 13244299124 scopus 로고    scopus 로고
    • Applying Support Vector Machines for Gene Ontology based gene function prediction
    • Vinayagam A, et al. (2004) Applying Support Vector Machines for Gene Ontology based gene function prediction. BMC Bioinformatics 5:116.
    • (2004) BMC Bioinformatics , vol.5 , pp. 116
    • Vinayagam, A.1
  • 17
    • 0043122923 scopus 로고    scopus 로고
    • OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms
    • Zehetner G (2003) OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. Nucleic Acids Res 31(13):3799-3803.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3799-3803
    • Zehetner, G.1
  • 18
    • 0033452362 scopus 로고    scopus 로고
    • Prediction of gene function by genome-scale expression analysis: Prostate cancer-associated genes
    • DOI 10.1101/gr.9.12.1198
    • Walker MG, Volkmuth W, Sprinzak E, Hodgson D, Klingler T (1999) Prediction of gene function by genome-scale expression analysis: Prostate cancer-associated genes. Genome Res 9(12):1198-1203. (Pubitemid 30042503)
    • (1999) Genome Research , vol.9 , Issue.12 , pp. 1198-1203
    • Walker, M.G.1    Volkmuth, W.2    Sprinzak, E.3    Hodgson, D.4    Klingler, T.5
  • 19
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, and open problems
    • DOI 10.1093/bioinformatics/bti565
    • Khatri P, Drǎghici S (2005) Ontological analysis of gene expression data: Current tools, limitations, and open problems. Bioinformatics 21(18):3587-3595. (Pubitemid 41264092)
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 21
    • 54949120643 scopus 로고    scopus 로고
    • Improving subcellular localization prediction using text classification and the gene ontology
    • Fyshe A, Liu Y, Szafron D, Greiner R, Lu P (2008) Improving subcellular localization prediction using text classification and the gene ontology. Bioinformatics 24(21):2512-2517.
    • (2008) Bioinformatics , vol.24 , Issue.21 , pp. 2512-2517
    • Fyshe, A.1    Liu, Y.2    Szafron, D.3    Greiner, R.4    Lu, P.5
  • 22
    • 84876122166 scopus 로고    scopus 로고
    • Protein function prediction using text-based features extracted from the biomedical literature: The CAFA challenge
    • Wong A, Shatkay H (2013) Protein function prediction using text-based features extracted from the biomedical literature: The CAFA challenge. BMC Bioinformatics 14(Suppl 3):S14.
    • (2013) BMC Bioinformatics , vol.14 , Issue.SUPPL. 3
    • Wong, A.1    Shatkay, H.2
  • 23
    • 56649094590 scopus 로고    scopus 로고
    • Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species
    • Lee K, et al. (2008) Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res 36(20):e136.
    • (2008) Nucleic Acids Res , vol.36 , Issue.20
    • Lee, K.1
  • 24
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási AL, Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5(2):101-113.
    • (2004) Nat Rev Genet , vol.5 , Issue.2 , pp. 101-113
    • Barabási, A.L.1    Oltvai, Z.N.2
  • 25
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan R, Ulitsky I, Shamir R (2007) Network-based prediction of protein function. Mol Syst Biol 3:88.
    • (2007) Mol Syst Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 26
    • 59849125136 scopus 로고    scopus 로고
    • Dynamic modularity in protein interaction networks predicts breast cancer outcome
    • Taylor IW, et al. (2009) Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 27(2):199-204.
    • (2009) Nat Biotechnol , vol.27 , Issue.2 , pp. 199-204
    • Taylor, I.W.1
  • 27
    • 84874947727 scopus 로고    scopus 로고
    • The BioGRID interaction database: 2013 Update
    • Chatr-Aryamontri A, et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res 41(Database Issue):D816-D823.
    • (2013) Nucleic Acids Res , vol.41 , Issue.DATABASE ISSUE
    • Chatr-Aryamontri, A.1
  • 28
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios I, et al. (2002) DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30(1):303-305. (Pubitemid 34679570)
    • (2002) Nucleic Acids Research , vol.30 , Issue.1 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.-M.5    Eisenberg, D.6
  • 31
    • 56649094590 scopus 로고    scopus 로고
    • Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species
    • Lee K, et al. (2008) Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res 36(20):e136.
    • (2008) Nucleic Acids Res , vol.36 , Issue.20
    • Lee, K.1
  • 32
    • 77953224209 scopus 로고    scopus 로고
    • Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets
    • Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T (2010) Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. Plant Cell 22(4):997-1005.
    • (2010) Plant Cell , vol.22 , Issue.4 , pp. 997-1005
    • Lee, K.1    Thorneycroft, D.2    Achuthan, P.3    Hermjakob, H.4    Ideker, T.5
  • 33
    • 79953032790 scopus 로고    scopus 로고
    • A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny
    • Wang Z, et al. (2011) A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS ONE 6(3):e17906.
    • (2011) PLoS ONE , vol.6 , Issue.3
    • Wang, Z.1
  • 34
    • 0032411723 scopus 로고    scopus 로고
    • The genetics of disulfide bond metabolism
    • DOI 10.1146/annurev.genet.32.1.163
    • Rietsch A, Beckwith J (1998) The genetics of disulfide bond metabolism. Annu Rev Genet 32:163-184. (Pubitemid 29045311)
    • (1998) Annual Review of Genetics , vol.32 , pp. 163-184
    • Rietsch, A.1    Beckwith, J.2
  • 35
    • 70350504453 scopus 로고    scopus 로고
    • The DNA-damage response in human biology and disease
    • Jackson SP, Bartek J (2009) The DNA-damage response in human biology and disease. Nature 461(7267):1071-1078.
    • (2009) Nature , vol.461 , Issue.7267 , pp. 1071-1078
    • Jackson, S.P.1    Bartek, J.2
  • 37
    • 17044383805 scopus 로고    scopus 로고
    • Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage
    • Takagi Y, et al. (2005) Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage. Mol Cell 18(2):237-243.
    • (2005) Mol Cell , vol.18 , Issue.2 , pp. 237-243
    • Takagi, Y.1
  • 38
    • 84881174691 scopus 로고    scopus 로고
    • Proteome-wide discovery of mislocated proteins in cancer
    • Lee K, et al. (2013) Proteome-wide discovery of mislocated proteins in cancer. Genome Res 23(8):1283-1294.
    • (2013) Genome Res , vol.23 , Issue.8 , pp. 1283-1294
    • Lee, K.1
  • 42
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gasch AP, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241-4257.
    • (2000) Mol Biol Cell , vol.11 , Issue.12 , pp. 4241-4257
    • Gasch, A.P.1
  • 43
    • 0028363566 scopus 로고
    • INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter
    • Ambroziak J, Henry SA (1994) INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 269(21):15344-15349. (Pubitemid 24198387)
    • (1994) Journal of Biological Chemistry , vol.269 , Issue.21 , pp. 15344-15349
    • Ambroziak, J.1    Henry, S.A.2
  • 44
    • 0029149344 scopus 로고
    • DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor: Structural requirements as defined by saturation mutagenesis
    • Schüller HJ, Richter K, Hoffmann B, Ebbert R, Schweizer E (1995) DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor: Structural requirements as defined by saturation mutagenesis. FEBS Lett 370(1-2):149-152.
    • (1995) FEBS Lett , vol.370 , Issue.1-2 , pp. 149-152
    • Schüller, H.J.1    Richter, K.2    Hoffmann, B.3    Ebbert, R.4    Schweizer, E.5
  • 45
    • 34548680957 scopus 로고    scopus 로고
    • Bimolecular fluorescence complementation analysis system for in vivo detection of protein-protein interaction in Saccharomyces cerevisiae
    • Sung MK, Huh WK (2007) Bimolecular fluorescence complementation analysis system for in vivo detection of protein-protein interaction in Saccharomyces cerevisiae. Yeast 24(9):767-775.
    • (2007) Yeast , vol.24 , Issue.9 , pp. 767-775
    • Sung, M.K.1    Huh, W.K.2
  • 46
    • 79952355184 scopus 로고    scopus 로고
    • Rapamycin increases rDNA stability by enhancing association of Sir2 with rDNA in Saccharomyces cerevisiae
    • Ha CW, Huh WK (2011) Rapamycin increases rDNA stability by enhancing association of Sir2 with rDNA in Saccharomyces cerevisiae. Nucleic Acids Res 39(4):1336-1350.
    • (2011) Nucleic Acids Res , vol.39 , Issue.4 , pp. 1336-1350
    • Ha, C.W.1    Huh, W.K.2
  • 47
    • 84859024732 scopus 로고    scopus 로고
    • Novel urinary protein biomarkers predicting the development of microalbuminuria and renal function decline in type 1 diabetes
    • Schlatzer D, et al. (2012) Novel urinary protein biomarkers predicting the development of microalbuminuria and renal function decline in type 1 diabetes. Diabetes Care 35(3):549-555.
    • (2012) Diabetes Care , vol.35 , Issue.3 , pp. 549-555
    • Schlatzer, D.1


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