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Volumn 3, Issue 5, 2005, Pages 0815-0825

Systematic association of genes to phenotypes by genome and literature mining

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA BASE; DEGRADATION; FOOD POISONING; FOOD SPOILAGE; GENE CLUSTER; GENETIC ANALYSIS; GENOME; MEDICAL LITERATURE; MEDLINE; NONHUMAN; PHENOTYPE; PROKARYOTE; STATISTICAL SIGNIFICANCE; BACTERIUM; COMPARATIVE STUDY; ENZYMOLOGY; GENE; GENETIC DATABASE; GENETICS; GENOTYPE; HUMAN; MICROBIOLOGY; PLANT; PUBLISHING;

EID: 21844471754     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030134     Document Type: Article
Times cited : (130)

References (58)
  • 2
    • 0032502899 scopus 로고    scopus 로고
    • Differential genome analysis applied to the species-specific features of Helicobacter pylori
    • Huynen M, Dandekar T, Bork P (1998) Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett 426: 1-5.
    • (1998) FEBS Lett , vol.426 , pp. 1-5
    • Huynen, M.1    Dandekar, T.2    Bork, P.3
  • 3
    • 0037383069 scopus 로고    scopus 로고
    • Potential genomic determinants of hyperthermophily
    • Makarova KS, Wolf YI, Koonin EV (2003) Potential genomic determinants of hyperthermophily. Trends Genet 19: 172-176.
    • (2003) Trends Genet , vol.19 , pp. 172-176
    • Makarova, K.S.1    Wolf, Y.I.2    Koonin, E.V.3
  • 4
    • 0346505465 scopus 로고    scopus 로고
    • A cross-genomic approach for systematic mapping of phenotypic traits to genes
    • Jim K, Parmar K, Singh M, Tavazoie S (2004) A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res 14: 109-115.
    • (2004) Genome Res , vol.14 , pp. 109-115
    • Jim, K.1    Parmar, K.2    Singh, M.3    Tavazoie, S.4
  • 5
    • 0037458108 scopus 로고    scopus 로고
    • Trait-to-gene: A computational method for predicting the function of uncharacterized genes
    • Levesque M, Shasha D, Kim W, Surette MG, Benfey PN (2003) Trait-to-gene: A computational method for predicting the function of uncharacterized genes. Curr Biol 13: 129-133.
    • (2003) Curr Biol , vol.13 , pp. 129-133
    • Levesque, M.1    Shasha, D.2    Kim, W.3    Surette, M.G.4    Benfey, P.N.5
  • 8
    • 0037250152 scopus 로고    scopus 로고
    • STRING: A database of predicted functional associations between proteins
    • von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, et al. (2003) STRING: A database of predicted functional associations between proteins. Nucleic Acids Res 31: 258-261.
    • (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
  • 10
    • 0037376106 scopus 로고    scopus 로고
    • Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: Clues for evolution and pathogenicity
    • Buchrieser C, Rusniok C, Kunst F, Cossart P, Glaser P (2003) Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: Clues for evolution and pathogenicity. FEMS Immunol Med Microbiol 35: 207-213.
    • (2003) FEMS Immunol Med Microbiol , vol.35 , pp. 207-213
    • Buchrieser, C.1    Rusniok, C.2    Kunst, F.3    Cossart, P.4    Glaser, P.5
  • 11
    • 0030950716 scopus 로고    scopus 로고
    • Bacterial phospholipases and their role in virulence
    • Songer JG (1997) Bacterial phospholipases and their role in virulence. Trends Microbiol 5: 156-161.
    • (1997) Trends Microbiol , vol.5 , pp. 156-161
    • Songer, J.G.1
  • 12
    • 1042298781 scopus 로고    scopus 로고
    • Role of Clostridium perfringens phospholipase C in the pathogenesis of gas gangrene
    • Flores-Diaz M, Alape-Giron A (2003) Role of Clostridium perfringens phospholipase C in the pathogenesis of gas gangrene. Toxicon 42: 979-986.
    • (2003) Toxicon , vol.42 , pp. 979-986
    • Flores-Diaz, M.1    Alape-Giron, A.2
  • 13
    • 0035216679 scopus 로고    scopus 로고
    • A sigma(54)-dependent PTS permease of the mannose family is responsible for sensitivity of Listeria monocytogenes to mesentericin Y105
    • Dalet K, Cenatiempo Y, Cossart P, Hechard Y (2001) A sigma(54)-dependent PTS permease of the mannose family is responsible for sensitivity of Listeria monocytogenes to mesentericin Y105. Microbiology 147: 3263-3269.
    • (2001) Microbiology , vol.147 , pp. 3263-3269
    • Dalet, K.1    Cenatiempo, Y.2    Cossart, P.3    Hechard, Y.4
  • 14
    • 0032851358 scopus 로고    scopus 로고
    • The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins
    • Kofoid E, Rappleye C, Stojiljkovic I, Roth J (1999) The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181: 5317-5329.
    • (1999) J Bacteriol , vol.181 , pp. 5317-5329
    • Kofoid, E.1    Rappleye, C.2    Stojiljkovic, I.3    Roth, J.4
  • 16
    • 0002229692 scopus 로고
    • Biogenic amines in lactic acid-fermented vegetables
    • Anderson R (1988) Biogenic amines in lactic acid-fermented vegetables. Lebensm-Wiss u Technol 21: 68-69.
    • (1988) Lebensm-Wiss U Technol , vol.21 , pp. 68-69
    • Anderson, R.1
  • 17
    • 0026241219 scopus 로고
    • Mechanisms of formation of chloropropanols present in protein hydrolysates
    • Collier PD, Cromiue DDO, Davies AP (1991) Mechanisms of formation of chloropropanols present in protein hydrolysates. J Am Oil Chem Soc 68: 785-790.
    • (1991) J Am Oil Chem Soc , vol.68 , pp. 785-790
    • Collier, P.D.1    Cromiue, D.D.O.2    Davies, A.P.3
  • 19
    • 0033292011 scopus 로고    scopus 로고
    • Automatic extraction of biological information from scientific text: Protein-protein interactions
    • Blaschke C, Andrade MA, Ouzounis C, Valencia A (1999) Automatic extraction of biological information from scientific text: Protein-protein interactions. Proc Int Conf Intell Syst Mol Biol 7: 60-67.
    • (1999) Proc Int Conf Intell Syst Mol Biol , vol.7 , pp. 60-67
    • Blaschke, C.1    Andrade, M.A.2    Ouzounis, C.3    Valencia, A.4
  • 21
    • 0036649742 scopus 로고    scopus 로고
    • Association of genes to genetically inherited diseases using data mining
    • Perez-Iratxeta C, Bork P, Andrade MA (2002) Association of genes to genetically inherited diseases using data mining. Nat Genet 31: 316-319.
    • (2002) Nat Genet , vol.31 , pp. 316-319
    • Perez-Iratxeta, C.1    Bork, P.2    Andrade, M.A.3
  • 22
    • 0033758756 scopus 로고    scopus 로고
    • Pathogenicity islands and the evolution of microbes
    • Hacker J, Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54: 641-679.
    • (2000) Annu Rev Microbiol , vol.54 , pp. 641-679
    • Hacker, J.1    Kaper, J.B.2
  • 23
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem Sci 23: 324-328.
    • (1998) Trends Biochem Sci , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 25
    • 3042703044 scopus 로고    scopus 로고
    • Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs
    • Korbel JO, Jensen LJ, von Mering C, Bork P (2004) Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol 22: 911-917.
    • (2004) Nat Biotechnol , vol.22 , pp. 911-917
    • Korbel, J.O.1    Jensen, L.J.2    Von Mering, C.3    Bork, P.4
  • 26
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 27
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, et al. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
    • (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
  • 28
    • 14844329372 scopus 로고    scopus 로고
    • Ranking the whole MEDLINE database according to a large training set using text indexing
    • In press
    • Suomela BP, Andrade MA (2005) Ranking the whole MEDLINE database according to a large training set using text indexing. BMC Bioinformatics. In press.
    • (2005) BMC Bioinformatics
    • Suomela, B.P.1    Andrade, M.A.2
  • 30
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 32
    • 0039134476 scopus 로고
    • Algorithm {AS 152}: Cumulative hypergeometric probabilities
    • Lund RE (1980) Algorithm {AS 152}: Cumulative hypergeometric probabilities. Appl Statist 29: 221-223.
    • (1980) Appl Statist , vol.29 , pp. 221-223
    • Lund, R.E.1
  • 33
    • 0039726820 scopus 로고
    • Remark {AS R77}: A remark on algorithm {AS 152}: Cumulative hypergeometric probabilities
    • Shea BL (1989) Remark {AS R77}: A remark on algorithm {AS 152}: Cumulative hypergeometric probabilities. Appl Statist 38: 199-204.
    • (1989) Appl Statist , vol.38 , pp. 199-204
    • Shea, B.L.1
  • 34
    • 0242416999 scopus 로고    scopus 로고
    • Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
    • Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, et al. (2003) Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun 71: 2775-2786.
    • (2003) Infect Immun , vol.71 , pp. 2775-2786
    • Wei, J.1    Goldberg, M.B.2    Burland, V.3    Venkatesan, M.M.4    Deng, W.5
  • 35
    • 0034618559 scopus 로고    scopus 로고
    • Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
    • Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81-86.
    • (2000) Nature , vol.407 , pp. 81-86
    • Shigenobu, S.1    Watanabe, H.2    Hattori, M.3    Sakaki, Y.4    Ishikawa, H.5
  • 36
    • 0023664370 scopus 로고
    • Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon
    • Yamada M, Saier MH Jr (1987) Glucitol-specific enzymes of the phosphotransferase system in Escherichia coli. Nucleotide sequence of the gut operon. J Biol Chem 262: 5455-5463.
    • (1987) J Biol Chem , vol.262 , pp. 5455-5463
    • Yamada, M.1    Saier Jr., M.H.2
  • 37
    • 0028870094 scopus 로고
    • The vanZ gene of Tn1546 from Enterococcus faecium BM4147 confers resistance to teicoplanin
    • Arthur M, Depardieu F, Molinas C, Reynolds P, Courvalin P (1995) The vanZ gene of Tn1546 from Enterococcus faecium BM4147 confers resistance to teicoplanin. Gene 154: 87-92.
    • (1995) Gene , vol.154 , pp. 87-92
    • Arthur, M.1    Depardieu, F.2    Molinas, C.3    Reynolds, P.4    Courvalin, P.5
  • 38
    • 0027382981 scopus 로고
    • Sequence and arrangement of two genes of the butyrate-synthesis pathway of Clostridium acetobutylicum ATCC 824
    • Walter KA, Nair RV, Cary JW, Bennett GN, Papoutsakis ET (1993) Sequence and arrangement of two genes of the butyrate-synthesis pathway of Clostridium acetobutylicum ATCC 824. Gene 134: 107-111.
    • (1993) Gene , vol.134 , pp. 107-111
    • Walter, K.A.1    Nair, R.V.2    Cary, J.W.3    Bennett, G.N.4    Papoutsakis, E.T.5
  • 39
    • 0027815162 scopus 로고
    • Bacillus subtilis flagellar proteins FliP, FliQ, FliR and FlhB are related to Shigella flexneri virulence factors
    • Carpenter PB, Zuberi AR, Ordal GW (1993) Bacillus subtilis flagellar proteins FliP, FliQ, FliR and FlhB are related to Shigella flexneri virulence factors. Gene 137: 243-245.
    • (1993) Gene , vol.137 , pp. 243-245
    • Carpenter, P.B.1    Zuberi, A.R.2    Ordal, G.W.3
  • 40
    • 0022449962 scopus 로고
    • Nucleotide sequence corresponding to five chemotaxis genes in Escherichia coli
    • Mutoh N, Simon MI (1986) Nucleotide sequence corresponding to five chemotaxis genes in Escherichia coli. J Bacteriol 165: 161-166.
    • (1986) J Bacteriol , vol.165 , pp. 161-166
    • Mutoh, N.1    Simon, M.I.2
  • 41
    • 0036066821 scopus 로고    scopus 로고
    • Functional characterization of Gne (UDP-N-acetylglucosamine-4-epimerase), Wzz (chain length determinant), and Wzy (O-antigen polymerase) of Yersinia enterocolitica serotype O:8
    • Bengoechea JA, Pinta E, Salminen T, Oertelt C, Holst O, et al. (2002) Functional characterization of Gne (UDP-N-acetylglucosamine-4-epimerase), Wzz (chain length determinant), and Wzy (O-antigen polymerase) of Yersinia enterocolitica serotype O:8. J Bacteriol 184: 4277-4287.
    • (2002) J Bacteriol , vol.184 , pp. 4277-4287
    • Bengoechea, J.A.1    Pinta, E.2    Salminen, T.3    Oertelt, C.4    Holst, O.5
  • 42
    • 0027255396 scopus 로고
    • Molecular analysis of region 1 of the Escherichia coli K5 antigen gene cluster: A region encoding proteins involved in cell surface expression of capsular polysaccharide
    • Pazzani C, Rosenow C, Boulnois GJ, Bronner D, Jann K, et al. (1993) Molecular analysis of region 1 of the Escherichia coli K5 antigen gene cluster: A region encoding proteins involved in cell surface expression of capsular polysaccharide. J Bacteriol 175: 5978-5983.
    • (1993) J Bacteriol , vol.175 , pp. 5978-5983
    • Pazzani, C.1    Rosenow, C.2    Boulnois, G.J.3    Bronner, D.4    Jann, K.5
  • 44
    • 0033020793 scopus 로고    scopus 로고
    • Pseudomonas aeruginosa fur overlaps with a gene encoding a novel outer membrane lipoprotein, OmlA
    • Ochsner UA, Vasil AI, Johnson Z, Vasil ML (1999) Pseudomonas aeruginosa fur overlaps with a gene encoding a novel outer membrane lipoprotein, OmlA. J Bacteriol 181: 1099-1109.
    • (1999) J Bacteriol , vol.181 , pp. 1099-1109
    • Ochsner, U.A.1    Vasil, A.I.2    Johnson, Z.3    Vasil, M.L.4
  • 45
    • 0025163439 scopus 로고
    • E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo
    • Ross W, Thompson JF, Newlands JT, Gourse RL (1990) E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo.EMBO J 9: 3733-3742.
    • (1990) EMBO J , vol.9 , pp. 3733-3742
    • Ross, W.1    Thompson, J.F.2    Newlands, J.T.3    Gourse, R.L.4
  • 46
    • 0028314541 scopus 로고
    • Multidrug resistance pumps in bacteria: Variations on a theme
    • Lewis K (1994) Multidrug resistance pumps in bacteria: Variations on a theme. Trends Biochem Sci 19: 119-123.
    • (1994) Trends Biochem Sci , vol.19 , pp. 119-123
    • Lewis, K.1
  • 47
    • 0019122021 scopus 로고
    • The effect of netilmicin and other aminoglycosides on renal function. A survey of the literature on the nephrotoxicity of netilmicin
    • Dahlager JI (1980) The effect of netilmicin and other aminoglycosides on renal function. A survey of the literature on the nephrotoxicity of netilmicin. Scand J Infect Dis Suppl 23: 96-102.
    • (1980) Scand J Infect Dis Suppl , vol.23 , pp. 96-102
    • Dahlager, J.I.1
  • 48
    • 0029988098 scopus 로고    scopus 로고
    • X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme
    • Pares S, Mouz N, Petillot Y, Hakenbeck R, Dideberg O (1996) X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme. Nat Struct Biol 3: 284-289.
    • (1996) Nat Struct Biol , vol.3 , pp. 284-289
    • Pares, S.1    Mouz, N.2    Petillot, Y.3    Hakenbeck, R.4    Dideberg, O.5
  • 49
    • 0022649029 scopus 로고
    • spoIID operon of Bacillus subtilis: Cloning and sequence
    • Lopez-Diaz I, Clarke S, Mandelstam J (1986) spoIID operon of Bacillus subtilis: cloning and sequence. J Gen Microbiol 132 (Pt 2): 341-354.
    • (1986) J Gen Microbiol , vol.132 , Issue.2 PART , pp. 341-354
    • Lopez-Diaz, I.1    Clarke, S.2    Mandelstam, J.3
  • 50
    • 0033167939 scopus 로고    scopus 로고
    • Cyanophycinase, a peptidase degrading the cyanobacterial reserve material multi-L-arginylpoly-L-aspartic acid (cyanophycin): Molecular cloning of the gene of Synechocystis sp. PCC 6803, expression in Escherichia coli, and biochemical characterization of the purified enzyme
    • Richter R, Hejazi M, Kraft R, Ziegler K, Lockau W (1999) Cyanophycinase, a peptidase degrading the cyanobacterial reserve material multi-L-arginylpoly-L- aspartic acid (cyanophycin): Molecular cloning of the gene of Synechocystis sp. PCC 6803, expression in Escherichia coli, and biochemical characterization of the purified enzyme. Eur J Biochem 263: 163-169.
    • (1999) Eur J Biochem , vol.263 , pp. 163-169
    • Richter, R.1    Hejazi, M.2    Kraft, R.3    Ziegler, K.4    Lockau, W.5
  • 52
    • 0033979067 scopus 로고    scopus 로고
    • Complete sporecortex hydrolysis during germination of Bacillus subtilis 168 requires SleB and YpeB
    • Boland FM, Atrih A, Chirakkal H, Foster SJ, Moir A (2000) Complete sporecortex hydrolysis during germination of Bacillus subtilis 168 requires SleB and YpeB. Microbiology 146 (Pt 1): 57-64.
    • (2000) Microbiology , vol.146 , Issue.1 PART , pp. 57-64
    • Boland, F.M.1    Atrih, A.2    Chirakkal, H.3    Foster, S.J.4    Moir, A.5
  • 53
    • 0037727706 scopus 로고    scopus 로고
    • Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases
    • Rigden DJ, Jedrzejas MJ, Galperin MY (2003) Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases. Trends Biochem Sci 28: 230-234.
    • (2003) Trends Biochem Sci , vol.28 , pp. 230-234
    • Rigden, D.J.1    Jedrzejas, M.J.2    Galperin, M.Y.3
  • 54
    • 0032734702 scopus 로고    scopus 로고
    • Molecular characterization of femA from Staphylococcus hominis and Staphylococcus saprophyticus, and femA-based discrimination of staphylococcal species
    • Vannuffel P, Heusterspreute M, Bouyer M, Vandercam B, Philippe M, et al. (1999) Molecular characterization of femA from Staphylococcus hominis and Staphylococcus saprophyticus, and femA-based discrimination of staphylococcal species. Res Microbiol 150: 129-141.
    • (1999) Res Microbiol , vol.150 , pp. 129-141
    • Vannuffel, P.1    Heusterspreute, M.2    Bouyer, M.3    Vandercam, B.4    Philippe, M.5
  • 55
    • 0028361562 scopus 로고
    • A reverse gyrase with an unusual structure. A type I DNA topoisomerase from the hyperthermophile Methanopyrus kandleri is a two-subunit protein
    • Kozyavkin SA, Krah R, Gellert M, Stetter KO, Lake JA, et al. (1994) A reverse gyrase with an unusual structure. A type I DNA topoisomerase from the hyperthermophile Methanopyrus kandleri is a two-subunit protein. J Biol Chem 269: 11081-11089.
    • (1994) J Biol Chem , vol.269 , pp. 11081-11089
    • Kozyavkin, S.A.1    Krah, R.2    Gellert, M.3    Stetter, K.O.4    Lake, J.A.5
  • 56
    • 4143101682 scopus 로고    scopus 로고
    • Chemotaxis-guided movements in bacteria
    • Lux R, Shi W (2004) Chemotaxis-guided movements in bacteria. Crit Rev Oral Biol Med 15: 207-220.
    • (2004) Crit Rev Oral Biol Med , vol.15 , pp. 207-220
    • Lux, R.1    Shi, W.2
  • 58
    • 4344716137 scopus 로고    scopus 로고
    • A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium
    • Kelly A, Goldberg MD, Carroll RK, Danino V, Hinton JC, et al. (2004) A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology 150: 2037-2053.
    • (2004) Microbiology , vol.150 , pp. 2037-2053
    • Kelly, A.1    Goldberg, M.D.2    Carroll, R.K.3    Danino, V.4    Hinton, J.C.5


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